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
151	0.02561	0.5485	b4041	plsB	-9.39	0.134646	197 -- 210	74 -- 86	glycerol-3-phosphate O-acyltransferase	_____________196____________211\n_____________\|______________\|\n5'-UCG...ACAUC________CC____GGCCA...UGG-3'\n______________GUUUAUGU__GGCU\n______________\|\|\|:\|:\|\|__\|\|\|\|\n______________CAAGUGCA__CCGA\n3'-CGC...GUUUU________A_____AAUCA...AAG-5'\n_____________\|______________\|\n_____________87_____________73\n	198 -- 204	79 -- 85	-13.0466 kcal/mol	3.14742 kcal/mol	0.513318 kcal/mol	196 211@LB@ \| \|@LB@5'-UCG...ACAUC CC GGCCA...UGG-3'@LB@ GUUUAUGU GGCU@LB@ \|\|\|:\|:\|\| \|\|\|\|@LB@ CAAGUGCA CCGA@LB@3'-CGC...GUUUU A AAUCA...AAG-5'@LB@ \| \|@LB@ 87 73@LB@@LB@@LB@Energy -9.39 kcal/mol@LB@Hybridization Energy -13.0466 kcal/mol@LB@Unfolding Energy - mRNA 3.14742 kcal/mol@LB@Unfolding Energy - sRNA 0.513318 kcal/mol@LB@@LB@Position - mRNA 197 -- 210@LB@Position - sRNA 74 -- 86@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 79 -- 85@LB@
152	0.02564	0.5485	b0887	cydD	-10.22	0.096853	263 -- 271	74 -- 82	glutathione/cysteine ABC transporter export permease/ATPase	_____________262_______272\n_____________\|_________\|\n5'-AUU...UCCCA_________GAAUA...UGA-3'\n______________ACGUUGGCU\n______________\|\|\|\|\|\|\|\|\|\n______________UGCAACCGA\n3'-CGC...UCAAG_________AAUCA...AAG-5'\n_____________\|_________\|\n_____________83________73\n	265 -- 271	74 -- 80	-15.056 kcal/mol	4.4924 kcal/mol	0.342466 kcal/mol	262 272@LB@ \| \|@LB@5'-AUU...UCCCA GAAUA...UGA-3'@LB@ ACGUUGGCU@LB@ \|\|\|\|\|\|\|\|\|@LB@ UGCAACCGA@LB@3'-CGC...UCAAG AAUCA...AAG-5'@LB@ \| \|@LB@ 83 73@LB@@LB@@LB@Energy -10.22 kcal/mol@LB@Hybridization Energy -15.056 kcal/mol@LB@Unfolding Energy - mRNA 4.4924 kcal/mol@LB@Unfolding Energy - sRNA 0.342466 kcal/mol@LB@@LB@Position - mRNA 263 -- 271@LB@Position - sRNA 74 -- 82@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 74 -- 80@LB@
153	0.02565	0.5485	b2764	cysJ	-8.62	0.180864	16 -- 26	74 -- 84	sulfite reductase alpha subunit flavoprotein	_____________15__________27\n_____________\|___________\|\n5'-UUC...UUUCA___G_______AAUCU...UUG-3'\n______________UUA_GUUGGUU\n______________\|:\|_\|\|\|\|\|:\|\n______________AGU_CAACCGA\n3'-CGC...UUUCA___G_______AAUCA...AAG-5'\n_____________\|___________\|\n_____________85__________73\n	20 -- 26	74 -- 80	-11.948 kcal/mol	2.81948 kcal/mol	0.508159 kcal/mol	15 27@LB@ \| \|@LB@5'-UUC...UUUCA G AAUCU...UUG-3'@LB@ UUA GUUGGUU@LB@ \|:\| \|\|\|\|\|:\|@LB@ AGU CAACCGA@LB@3'-CGC...UUUCA G AAUCA...AAG-5'@LB@ \| \|@LB@ 85 73@LB@@LB@@LB@Energy -8.62 kcal/mol@LB@Hybridization Energy -11.948 kcal/mol@LB@Unfolding Energy - mRNA 2.81948 kcal/mol@LB@Unfolding Energy - sRNA 0.508159 kcal/mol@LB@@LB@Position - mRNA 16 -- 26@LB@Position - sRNA 74 -- 84@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 74 -- 80@LB@
154	0.02609	0.5541	b4195	ulaC	-15.85	0.009707	6 -- 31	56 -- 80	L-ascorbate-specific enzyme IIA component of PTS	_____________5__________________________32\n_____________\|__________________________\|\n______5'-GCGCG______GAGUACAAAAG_________UGGCG...UGG-3'\n______________GUUGGC___________CGAGUUGAG\n______________\|\|\|\|\|\|___________\|\|\|\|\|\|\|\|\|\n______________CAACCG___________GCUCAACUC\n3'-CGC...AAGUG______AAAUCAAUAA__________UUUGA...AAG-5'\n_____________\|__________________________\|\n_____________81_________________________55\n	25 -- 31	56 -- 62	-23.4839 kcal/mol	5.91355 kcal/mol	1.71557 kcal/mol	5 32@LB@ \| \|@LB@ 5'-GCGCG GAGUACAAAAG UGGCG...UGG-3'@LB@ GUUGGC CGAGUUGAG@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ CAACCG GCUCAACUC@LB@3'-CGC...AAGUG AAAUCAAUAA UUUGA...AAG-5'@LB@ \| \|@LB@ 81 55@LB@@LB@@LB@Energy -15.85 kcal/mol@LB@Hybridization Energy -23.4839 kcal/mol@LB@Unfolding Energy - mRNA 5.91355 kcal/mol@LB@Unfolding Energy - sRNA 1.71557 kcal/mol@LB@@LB@Position - mRNA 6 -- 31@LB@Position - sRNA 56 -- 80@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 56 -- 62@LB@
155	0.02668	0.5559	b1625	cnu	-8.12	0.218326	240 -- 246	81 -- 87	nucleoid-associated oriC-binding protein; H-NS and StpA stabilizing factor	_____________239_____247\n_____________\|_______\|\n5'-UUU...AAAUC_______UCGAA...AUC-3'\n______________AGUUCAC\n______________\|\|\|\|\|\|\|\n______________UCAAGUG\n3'-CGC...CGUUU_______CAACC...AAG-5'\n_____________\|_______\|\n_____________88______80\n	240 -- 246	81 -- 87	-9.1905 kcal/mol	0.576286 kcal/mol	0.494577 kcal/mol	239 247@LB@ \| \|@LB@5'-UUU...AAAUC UCGAA...AUC-3'@LB@ AGUUCAC@LB@ \|\|\|\|\|\|\|@LB@ UCAAGUG@LB@3'-CGC...CGUUU CAACC...AAG-5'@LB@ \| \|@LB@ 88 80@LB@@LB@@LB@Energy -8.12 kcal/mol@LB@Hybridization Energy -9.1905 kcal/mol@LB@Unfolding Energy - mRNA 0.576286 kcal/mol@LB@Unfolding Energy - sRNA 0.494577 kcal/mol@LB@@LB@Position - mRNA 240 -- 246@LB@Position - sRNA 81 -- 87@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 81 -- 87@LB@
156	0.02672	0.5559	b0957	ompA	-9.60	0.124024	22 -- 30	81 -- 89	outer membrane protein A (3a;II*;G;d)	_____________21________31\n_____________\|_________\|\n5'-CUU...CUGAC_________ACUUG...AAC-3'\n______________GGAGUUCAC\n______________::\|\|\|\|\|\|\|\n______________UUUCAAGUG\n3'-CGC...GGCGU_________CAACC...AAG-5'\n_____________\|_________\|\n_____________90________80\n	24 -- 30	81 -- 87	-11.1644 kcal/mol	1.067 kcal/mol	0.501582 kcal/mol	21 31@LB@ \| \|@LB@5'-CUU...CUGAC ACUUG...AAC-3'@LB@ GGAGUUCAC@LB@ ::\|\|\|\|\|\|\|@LB@ UUUCAAGUG@LB@3'-CGC...GGCGU CAACC...AAG-5'@LB@ \| \|@LB@ 90 80@LB@@LB@@LB@Energy -9.60 kcal/mol@LB@Hybridization Energy -11.1644 kcal/mol@LB@Unfolding Energy - mRNA 1.067 kcal/mol@LB@Unfolding Energy - sRNA 0.501582 kcal/mol@LB@@LB@Position - mRNA 22 -- 30@LB@Position - sRNA 81 -- 89@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 81 -- 87@LB@
157	0.02703	0.5559	b3221	yhcH	-9.14	0.148013	119 -- 127	77 -- 85	DUF386 family protein cupin superfamily	_____________118_______128\n_____________\|_________\|\n5'-AUC...GGCAU_________AUUUA...AAG-3'\n______________UUCAUGUUG\n______________\|\|\|\|:\|\|\|\|\n______________AAGUGCAAC\n3'-CGC...UUUUC_________CGAAA...AAG-5'\n_____________\|_________\|\n_____________86________76\n	121 -- 127	77 -- 83	-10.7393 kcal/mol	1.16925 kcal/mol	0.427568 kcal/mol	118 128@LB@ \| \|@LB@5'-AUC...GGCAU AUUUA...AAG-3'@LB@ UUCAUGUUG@LB@ \|\|\|\|:\|\|\|\|@LB@ AAGUGCAAC@LB@3'-CGC...UUUUC CGAAA...AAG-5'@LB@ \| \|@LB@ 86 76@LB@@LB@@LB@Energy -9.14 kcal/mol@LB@Hybridization Energy -10.7393 kcal/mol@LB@Unfolding Energy - mRNA 1.16925 kcal/mol@LB@Unfolding Energy - sRNA 0.427568 kcal/mol@LB@@LB@Position - mRNA 119 -- 127@LB@Position - sRNA 77 -- 85@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 77 -- 83@LB@
158	0.02721	0.5559	b1724	ydiZ	-8.58	0.183444	272 -- 279	57 -- 64	uncharacterized protein	_____________271______280\n_____________\|________\|\n5'-UUU...AUUAA________AUAAU...ACG-3'\n______________CGAGUUGA\n______________\|\|\|\|\|\|\|\|\n______________GCUCAACU\n3'-CGC...AAUAA________CUUUG...AAG-5'\n_____________\|________\|\n_____________65_______56\n	273 -- 279	57 -- 63	-11.4752 kcal/mol	1.7639 kcal/mol	1.12823 kcal/mol	271 280@LB@ \| \|@LB@5'-UUU...AUUAA AUAAU...ACG-3'@LB@ CGAGUUGA@LB@ \|\|\|\|\|\|\|\|@LB@ GCUCAACU@LB@3'-CGC...AAUAA CUUUG...AAG-5'@LB@ \| \|@LB@ 65 56@LB@@LB@@LB@Energy -8.58 kcal/mol@LB@Hybridization Energy -11.4752 kcal/mol@LB@Unfolding Energy - mRNA 1.7639 kcal/mol@LB@Unfolding Energy - sRNA 1.12823 kcal/mol@LB@@LB@Position - mRNA 272 -- 279@LB@Position - sRNA 57 -- 64@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 57 -- 63@LB@
159	0.02757	0.5559	b2701	mltB	-11.73	0.052671	73 -- 129	32 -- 90	membrane-bound lytic murein transglycosylase B	_____________72_________________________________________________________________130\n_____________\|__________________________________________________________________\|\n5'-AGA...UGAAU_____GAUA___AG__GAA_________________UUAUGU___G_____UAU____________ACCGC...GAA-3'\n______________AAAAG____GCG__GG___________UGAGUUGAG______AAA_UC_CG___CGGGCAGUGACU\n______________\|\|\|\|\|____:\|\|__\|\|___________:\|\|\|\|\|\|\|\|______\|\|\|_\|\|_\|\|___\|\|\|\|\|\|\|\|\|\|\|\|\n______________UUUUC____UGC__CC___________GCUCAACUC______UUU_AG_GC___GCCCGUCACUGA\n3'-CGC...AGGCG_____AAG____AA__GAAAUCAAUAA__________________G__A__UUU____________AGUUC...AAG-5'\n_____________\|__________________________________________________________________\|\n_____________91_________________________________________________________________31\n	94 -- 100	56 -- 62	-46.1733 kcal/mol	15.4898 kcal/mol	18.9502 kcal/mol	72 130@LB@ \| \|@LB@5'-AGA...UGAAU GAUA AG GAA UUAUGU G UAU ACCGC...GAA-3'@LB@ AAAAG GCG GG UGAGUUGAG AAA UC CG CGGGCAGUGACU@LB@ \|\|\|\|\| :\|\| \|\| :\|\|\|\|\|\|\|\| \|\|\| \|\| \|\| \|\|\|\|\|\|\|\|\|\|\|\|@LB@ UUUUC UGC CC GCUCAACUC UUU AG GC GCCCGUCACUGA@LB@3'-CGC...AGGCG AAG AA GAAAUCAAUAA G A UUU AGUUC...AAG-5'@LB@ \| \|@LB@ 91 31@LB@@LB@@LB@Energy -11.73 kcal/mol@LB@Hybridization Energy -46.1733 kcal/mol@LB@Unfolding Energy - mRNA 15.4898 kcal/mol@LB@Unfolding Energy - sRNA 18.9502 kcal/mol@LB@@LB@Position - mRNA 73 -- 129@LB@Position - sRNA 32 -- 90@LB@Position Seed - mRNA 94 -- 100@LB@Position Seed - sRNA 56 -- 62@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@

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)

Job resubmission

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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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