Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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
141	0.02331	0.5385	b1844	exoX	-7.22	0.302733	200 -- 217	62 -- 83	exodeoxyribonuclease 10; DNA exonuclease X	_____________199_____________________218\n_____________\|_______________________\|\n5'-UUA...CAUGC_______C__A____________UACAG...UGA-3'\n______________CAUGUUG_GC_UUA_____UCGA\n______________\|\|:\|\|\|\|_\|\|_\|\|\|_____\|\|\|\|\n______________GUGCAAC_CG_AAU_____AGCU\n3'-CGC...UUCAA__________A___CAAUA____CAACU...AAG-5'\n_____________\|_______________________\|\n_____________84______________________61\n	200 -- 206	77 -- 83	-13.618 kcal/mol	4.77882 kcal/mol	1.62352 kcal/mol	199 218@LB@ \| \|@LB@5'-UUA...CAUGC C A UACAG...UGA-3'@LB@ CAUGUUG GC UUA UCGA@LB@ \|\|:\|\|\|\| \|\| \|\|\| \|\|\|\|@LB@ GUGCAAC CG AAU AGCU@LB@3'-CGC...UUCAA A CAAUA CAACU...AAG-5'@LB@ \| \|@LB@ 84 61@LB@@LB@@LB@Energy -7.22 kcal/mol@LB@Hybridization Energy -13.618 kcal/mol@LB@Unfolding Energy - mRNA 4.77882 kcal/mol@LB@Unfolding Energy - sRNA 1.62352 kcal/mol@LB@@LB@Position - mRNA 200 -- 217@LB@Position - sRNA 62 -- 83@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 77 -- 83@LB@
38	0.006978	0.5385	b3738	atpB	-10.53	0.085759	128 -- 143	69 -- 84	F0 sector of membrane-bound ATP synthase subunit a	_____________127______________144\n_____________\|________________\|\n5'-CAU...GAUCG______G_________GCUGG...ACC-3'\n______________UUACGU_GGUUUUGGU\n______________\|:\|\|\|\|_\|\|:\|\|\|:\|\|\n______________AGUGCA_CCGAAAUCA\n3'-CGC...UUUCA______A_________AUAAG...AAG-5'\n_____________\|________________\|\n_____________85_______________68\n	137 -- 143	69 -- 75	-16.8893 kcal/mol	5.79988 kcal/mol	0.563592 kcal/mol	127 144@LB@ \| \|@LB@5'-CAU...GAUCG G GCUGG...ACC-3'@LB@ UUACGU GGUUUUGGU@LB@ \|:\|\|\|\| \|\|:\|\|\|:\|\|@LB@ AGUGCA CCGAAAUCA@LB@3'-CGC...UUUCA A AUAAG...AAG-5'@LB@ \| \|@LB@ 85 68@LB@@LB@@LB@Energy -10.53 kcal/mol@LB@Hybridization Energy -16.8893 kcal/mol@LB@Unfolding Energy - mRNA 5.79988 kcal/mol@LB@Unfolding Energy - sRNA 0.563592 kcal/mol@LB@@LB@Position - mRNA 128 -- 143@LB@Position - sRNA 69 -- 84@LB@Position Seed - mRNA 137 -- 143@LB@Position Seed - sRNA 69 -- 75@LB@
8	0.001355	0.5385	b3915	fieF	-13.87	0.021962	2 -- 39	50 -- 90	ferrous iron and zinc transporter	_____________1_____________________________________________40\n_____________\|_____________________________________________\|\n__________5'-A_________U_____AA___A_____________A_U__C_____ACGUU...AUA-3'\n______________AAAAGUUCA_CGUUG__GCU________UUGAGU_G_AG_AACUC\n______________\|\|\|\|\|\|\|\|\|_\|\|\|\|\|__\|\|\|________\|:\|\|\|\|_\|_\|\|_\|\|\|\|\|\n______________UUUUCAAGU_GCAAC__CGA________AGCUCA_C_UC_UUGAG\n3'-CGC...AGGCG____________________AAUCAAUA______A____U_____AGCUU...AAG-5'\n_____________\|_____________________________________________\|\n_____________91____________________________________________49\n	4 -- 10	82 -- 88	-26.5193 kcal/mol	8.24047 kcal/mol	4.40801 kcal/mol	1 40@LB@ \| \|@LB@ 5'-A U AA A A U C ACGUU...AUA-3'@LB@ AAAAGUUCA CGUUG GCU UUGAGU G AG AACUC@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|\| \|\|\| \|:\|\|\|\| \| \|\| \|\|\|\|\|@LB@ UUUUCAAGU GCAAC CGA AGCUCA C UC UUGAG@LB@3'-CGC...AGGCG AAUCAAUA A U AGCUU...AAG-5'@LB@ \| \|@LB@ 91 49@LB@@LB@@LB@Energy -13.87 kcal/mol@LB@Hybridization Energy -26.5193 kcal/mol@LB@Unfolding Energy - mRNA 8.24047 kcal/mol@LB@Unfolding Energy - sRNA 4.40801 kcal/mol@LB@@LB@Position - mRNA 2 -- 39@LB@Position - sRNA 50 -- 90@LB@Position Seed - mRNA 4 -- 10@LB@Position Seed - sRNA 82 -- 88@LB@
47	0.009854	0.5385	b3408	feoA	-10.27	0.095129	159 -- 188	52 -- 83	ferrous iron transporter protein A	_____________158_________________________________189\n_____________\|___________________________________\|\n5'-AGC...CGCCC____A_______________C___UAA________AAGUA...CUG-3'\n______________CAUG__GGU___AGUUA_UC_AGU___UGAGAAAC\n______________\|\|:\|__\|\|:___\|\|\|\|\|_\|\|_\|\|\|___\|\|\|\|\|\|\|\|\n______________GUGC__CCG___UCAAU_AG_UCA___ACUCUUUG\n3'-CGC...UUCAA____AA___AAA_____A__C______________AGAGC...AAG-5'\n_____________\|___________________________________\|\n_____________84__________________________________51\n	182 -- 188	52 -- 58	-20.9255 kcal/mol	6.25891 kcal/mol	4.4004 kcal/mol	158 189@LB@ \| \|@LB@5'-AGC...CGCCC A C UAA AAGUA...CUG-3'@LB@ CAUG GGU AGUUA UC AGU UGAGAAAC@LB@ \|\|:\| \|\|: \|\|\|\|\| \|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ GUGC CCG UCAAU AG UCA ACUCUUUG@LB@3'-CGC...UUCAA AA AAA A C AGAGC...AAG-5'@LB@ \| \|@LB@ 84 51@LB@@LB@@LB@Energy -10.27 kcal/mol@LB@Hybridization Energy -20.9255 kcal/mol@LB@Unfolding Energy - mRNA 6.25891 kcal/mol@LB@Unfolding Energy - sRNA 4.4004 kcal/mol@LB@@LB@Position - mRNA 159 -- 188@LB@Position - sRNA 52 -- 83@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 52 -- 58@LB@
178	0.03115	0.5559	b2528	iscA	-9.66	0.120899	187 -- 207	62 -- 80	FeS cluster assembly protein	_____________186___________________208\n_____________\|_____________________\|\n5'-UUC...UAAGA____A_G_________G____UUACA...CCG-3'\n______________GUUG_G_UUUGGUUAU_UCGA\n______________\|\|\|\|_\|_\|\|\|:\|\|\|\|\|_\|\|\|\|\n______________CAAC_C_AAAUCAAUA_AGCU\n3'-CGC...AAGUG______G______________CAACU...AAG-5'\n_____________\|_____________________\|\n_____________81____________________61\n	196 -- 202	66 -- 72	-17.7068 kcal/mol	7.30815 kcal/mol	0.737855 kcal/mol	186 208@LB@ \| \|@LB@5'-UUC...UAAGA A G G UUACA...CCG-3'@LB@ GUUG G UUUGGUUAU UCGA@LB@ \|\|\|\| \| \|\|\|:\|\|\|\|\| \|\|\|\|@LB@ CAAC C AAAUCAAUA AGCU@LB@3'-CGC...AAGUG G CAACU...AAG-5'@LB@ \| \|@LB@ 81 61@LB@@LB@@LB@Energy -9.66 kcal/mol@LB@Hybridization Energy -17.7068 kcal/mol@LB@Unfolding Energy - mRNA 7.30815 kcal/mol@LB@Unfolding Energy - sRNA 0.737855 kcal/mol@LB@@LB@Position - mRNA 187 -- 207@LB@Position - sRNA 62 -- 80@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 66 -- 72@LB@
185	0.03283	0.5559	b1937	fliE	-12.05	0.046361	209 -- 229	14 -- 35	flagellar basal-body component	_____________208____________________230\n_____________\|______________________\|\n5'-CUG...UCAGC___A_______AUU________UAUCA...GUU-3'\n______________GAU__CAGGGG___GAAGGGGU\n______________\|\|:__\|\|:\|\|\|___:\|\|\|:\|\|\|\n______________CUG__GUUCCC___UUUCUCCA\n3'-CGC...CGUCA___AA______AAU________CGGCG...AAG-5'\n_____________\|______________________\|\n_____________36_____________________13\n	223 -- 229	14 -- 20	-20.5154 kcal/mol	5.13678 kcal/mol	3.33183 kcal/mol	208 230@LB@ \| \|@LB@5'-CUG...UCAGC A AUU UAUCA...GUU-3'@LB@ GAU CAGGGG GAAGGGGU@LB@ \|\|: \|\|:\|\|\| :\|\|\|:\|\|\|@LB@ CUG GUUCCC UUUCUCCA@LB@3'-CGC...CGUCA AA AAU CGGCG...AAG-5'@LB@ \| \|@LB@ 36 13@LB@@LB@@LB@Energy -12.05 kcal/mol@LB@Hybridization Energy -20.5154 kcal/mol@LB@Unfolding Energy - mRNA 5.13678 kcal/mol@LB@Unfolding Energy - sRNA 3.33183 kcal/mol@LB@@LB@Position - mRNA 209 -- 229@LB@Position - sRNA 14 -- 35@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 14 -- 20@LB@
180	0.03162	0.5559	b1941	fliI	-9.97	0.106944	57 -- 70	74 -- 88	flagellum-specific ATP synthase	_____________56______________71\n_____________\|_______________\|\n5'-CUG...ACCUU________A______GGCGC...GCG-3'\n______________AAGUUUGC__UGGCU\n______________\|\|\|\|\|::\|__\|\|\|\|\|\n______________UUCAAGUG__ACCGA\n3'-CGC...GCGUU________CA_____AAUCA...AAG-5'\n_____________\|_______________\|\n_____________89______________73\n	58 -- 64	81 -- 87	-13.0478 kcal/mol	2.55971 kcal/mol	0.516514 kcal/mol	56 71@LB@ \| \|@LB@5'-CUG...ACCUU A GGCGC...GCG-3'@LB@ AAGUUUGC UGGCU@LB@ \|\|\|\|\|::\| \|\|\|\|\|@LB@ UUCAAGUG ACCGA@LB@3'-CGC...GCGUU CA AAUCA...AAG-5'@LB@ \| \|@LB@ 89 73@LB@@LB@@LB@Energy -9.97 kcal/mol@LB@Hybridization Energy -13.0478 kcal/mol@LB@Unfolding Energy - mRNA 2.55971 kcal/mol@LB@Unfolding Energy - sRNA 0.516514 kcal/mol@LB@@LB@Position - mRNA 57 -- 70@LB@Position - sRNA 74 -- 88@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 81 -- 87@LB@
14	0.002739	0.5385	b0903	pflB	-11.82	0.050867	80 -- 105	57 -- 81	formate C-acetyltransferase 1 anaerobic; pyruvate formate-lyase 1	_____________79_________________________106\n_____________\|__________________________\|\n5'-CAC...AUUAU__G____GGUUU____G_________CAUAC...ACU-3'\n______________CG_UGGU_____GUUG_UUGGGUUGA\n______________\|\|_\|\|\|:_____\|\|\|:_\|:\|:\|\|\|\|\|\n______________GC_ACCG_____CAAU_AGCUCAACU\n3'-CGC...CAAGU__A____AAAU_____A_________CUUUG...AAG-5'\n_____________\|__________________________\|\n_____________82_________________________56\n	99 -- 105	57 -- 63	-19.5015 kcal/mol	6.38537 kcal/mol	1.29708 kcal/mol	79 106@LB@ \| \|@LB@5'-CAC...AUUAU G GGUUU G CAUAC...ACU-3'@LB@ CG UGGU GUUG UUGGGUUGA@LB@ \|\| \|\|\|: \|\|\|: \|:\|:\|\|\|\|\|@LB@ GC ACCG CAAU AGCUCAACU@LB@3'-CGC...CAAGU A AAAU A CUUUG...AAG-5'@LB@ \| \|@LB@ 82 56@LB@@LB@@LB@Energy -11.82 kcal/mol@LB@Hybridization Energy -19.5015 kcal/mol@LB@Unfolding Energy - mRNA 6.38537 kcal/mol@LB@Unfolding Energy - sRNA 1.29708 kcal/mol@LB@@LB@Position - mRNA 80 -- 105@LB@Position - sRNA 57 -- 81@LB@Position Seed - mRNA 99 -- 105@LB@Position Seed - sRNA 57 -- 63@LB@
160	0.02795	0.5559	b1475	fdnH	-7.98	0.230122	69 -- 80	24 -- 35	formate dehydrogenase-N Fe-S (beta) subunit nitrate-inducible	_____________68___________81\n_____________\|____________\|\n5'-CGC...ACUGG____________GUCGC...UUA-3'\n______________GGCUUUGAGGGU\n______________\|:\|\|\|::\|\|\|\|\|\n______________CUGAAGUUCCCA\n3'-CGC...CGUCA____________AUUUU...AAG-5'\n_____________\|____________\|\n_____________36___________23\n	74 -- 80	24 -- 30	-17.8377 kcal/mol	6.53052 kcal/mol	3.32971 kcal/mol	68 81@LB@ \| \|@LB@5'-CGC...ACUGG GUCGC...UUA-3'@LB@ GGCUUUGAGGGU@LB@ \|:\|\|\|::\|\|\|\|\|@LB@ CUGAAGUUCCCA@LB@3'-CGC...CGUCA AUUUU...AAG-5'@LB@ \| \|@LB@ 36 23@LB@@LB@@LB@Energy -7.98 kcal/mol@LB@Hybridization Energy -17.8377 kcal/mol@LB@Unfolding Energy - mRNA 6.53052 kcal/mol@LB@Unfolding Energy - sRNA 3.32971 kcal/mol@LB@@LB@Position - mRNA 69 -- 80@LB@Position - sRNA 24 -- 35@LB@Position Seed - mRNA 74 -- 80@LB@Position Seed - sRNA 24 -- 30@LB@
74	0.01362	0.5385	b0946	zapC	-12.02	0.046851	175 -- 197	15 -- 35	FtsZ stabilizer	_____________174_____________________198\n_____________\|_______________________\|\n5'-AUU...GCUGC_______U_____AG________CAGAU...GUU-3'\n______________GGUUUUA_AGGGU__GGGAGAGG\n______________\|::\|\|:\|_\|\|\|\|\|__:::\|\|\|\|\|\n______________CUGAAGU_UCCCA__UUUUCUCC\n3'-CGC...CGUCA_____________A_________ACGGC...AAG-5'\n_____________\|_______________________\|\n_____________36______________________14\n	191 -- 197	15 -- 21	-19.3355 kcal/mol	3.98393 kcal/mol	3.33058 kcal/mol	174 198@LB@ \| \|@LB@5'-AUU...GCUGC U AG CAGAU...GUU-3'@LB@ GGUUUUA AGGGU GGGAGAGG@LB@ \|::\|\|:\| \|\|\|\|\| :::\|\|\|\|\|@LB@ CUGAAGU UCCCA UUUUCUCC@LB@3'-CGC...CGUCA A ACGGC...AAG-5'@LB@ \| \|@LB@ 36 14@LB@@LB@@LB@Energy -12.02 kcal/mol@LB@Hybridization Energy -19.3355 kcal/mol@LB@Unfolding Energy - mRNA 3.98393 kcal/mol@LB@Unfolding Energy - sRNA 3.33058 kcal/mol@LB@@LB@Position - mRNA 175 -- 197@LB@Position - sRNA 15 -- 35@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 15 -- 21@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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