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
15	0.002894	0.5385	b2780	pyrG	-11.46	0.058961	111 -- 140	60 -- 90	CTP synthetase	_____________110_______________________________141\n_____________\|_________________________________\|\n5'-UGU...AUAAU________________ACA___CA_________AUACU...GCC-3'\n______________GAAAGUUUG___UGGC___GGU__UGUUCGGGU\n______________:\|\|\|\|\|\|::___\|\|\|\|___:\|\|__\|:\|\|\|\|:\|\|\n______________UUUUCAAGU___ACCG___UCA__AUAAGCUCA\n3'-CGC...AGGCG_________GCA____AAA______________ACUCU...AAG-5'\n_____________\|_________________________________\|\n_____________91________________________________59\n	134 -- 140	60 -- 66	-21.5125 kcal/mol	8.34782 kcal/mol	1.70935 kcal/mol	110 141@LB@ \| \|@LB@5'-UGU...AUAAU ACA CA AUACU...GCC-3'@LB@ GAAAGUUUG UGGC GGU UGUUCGGGU@LB@ :\|\|\|\|\|\|:: \|\|\|\| :\|\| \|:\|\|\|\|:\|\|@LB@ UUUUCAAGU ACCG UCA AUAAGCUCA@LB@3'-CGC...AGGCG GCA AAA ACUCU...AAG-5'@LB@ \| \|@LB@ 91 59@LB@@LB@@LB@Energy -11.46 kcal/mol@LB@Hybridization Energy -21.5125 kcal/mol@LB@Unfolding Energy - mRNA 8.34782 kcal/mol@LB@Unfolding Energy - sRNA 1.70935 kcal/mol@LB@@LB@Position - mRNA 111 -- 140@LB@Position - sRNA 60 -- 90@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 60 -- 66@LB@
23	0.004272	0.5385	b3315	rplV	-10.64	0.081808	245 -- 278	60 -- 90	50S ribosomal subunit protein L22	_____________244________________________________279\n_____________\|__________________________________\|\n5'-CGC...GCUCA__________C___UU___GACCUG_____C___AAGAA...UGG-3'\n______________GAAGGUUCGC_UUG__GCU______AUUCG_GGU\n______________:\|\|:\|\|\|\|:\|_\|\|\|__\|\|\|______\|\|\|\|\|_:\|\|\n______________UUUUCAAGUG_AAC__CGA______UAAGC_UCA\n3'-CGC...AGGCG__________C________AAUCAA_________ACUCU...AAG-5'\n_____________\|__________________________________\|\n_____________91_________________________________59\n	248 -- 254	81 -- 87	-21.0379 kcal/mol	8.68511 kcal/mol	1.70935 kcal/mol	244 279@LB@ \| \|@LB@5'-CGC...GCUCA C UU GACCUG C AAGAA...UGG-3'@LB@ GAAGGUUCGC UUG GCU AUUCG GGU@LB@ :\|\|:\|\|\|\|:\| \|\|\| \|\|\| \|\|\|\|\| :\|\|@LB@ UUUUCAAGUG AAC CGA UAAGC UCA@LB@3'-CGC...AGGCG C AAUCAA ACUCU...AAG-5'@LB@ \| \|@LB@ 91 59@LB@@LB@@LB@Energy -10.64 kcal/mol@LB@Hybridization Energy -21.0379 kcal/mol@LB@Unfolding Energy - mRNA 8.68511 kcal/mol@LB@Unfolding Energy - sRNA 1.70935 kcal/mol@LB@@LB@Position - mRNA 245 -- 278@LB@Position - sRNA 60 -- 90@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 81 -- 87@LB@
39	0.007274	0.5385	b1636	pdxY	-13.08	0.030384	230 -- 254	60 -- 84	pyridoxamine kinase	_____________229_______________________255\n_____________\|_________________________\|\n5'-UAU...CAGUC________U__A____C__G_____AACAG...UCU-3'\n______________UCACGUUG_UU_UGGU_AU_CGGGU\n______________\|\|\|\|\|\|\|\|_:\|_\|:\|\|_\|\|_\|\|:\|\|\n______________AGUGCAAC_GA_AUCA_UA_GCUCA\n3'-CGC...UUUCA________C__A____A__A_____ACUCU...AAG-5'\n_____________\|_________________________\|\n_____________85________________________59\n	231 -- 237	77 -- 83	-19.8659 kcal/mol	5.09201 kcal/mol	1.69371 kcal/mol	229 255@LB@ \| \|@LB@5'-UAU...CAGUC U A C G AACAG...UCU-3'@LB@ UCACGUUG UU UGGU AU CGGGU@LB@ \|\|\|\|\|\|\|\| :\| \|:\|\| \|\| \|\|:\|\|@LB@ AGUGCAAC GA AUCA UA GCUCA@LB@3'-CGC...UUUCA C A A A ACUCU...AAG-5'@LB@ \| \|@LB@ 85 59@LB@@LB@@LB@Energy -13.08 kcal/mol@LB@Hybridization Energy -19.8659 kcal/mol@LB@Unfolding Energy - mRNA 5.09201 kcal/mol@LB@Unfolding Energy - sRNA 1.69371 kcal/mol@LB@@LB@Position - mRNA 230 -- 254@LB@Position - sRNA 60 -- 84@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 77 -- 83@LB@
81	0.01462	0.5385	b3296	rpsD	-10.19	0.098165	202 -- 218	60 -- 78	30S ribosomal subunit protein S4	_____________201_________________219\n_____________\|___________________\|\n5'-AAG...GAAAA____A____A_________CCUAA...AAA-3'\n______________UGGC___AG_UAUUUGGGU\n______________\|\|\|\|___\|\|_\|\|\|\|:\|:\|\|\n______________ACCG___UC_AUAAGCUCA\n3'-CGC...GUGCA____AAA__A_________ACUCU...AAG-5'\n_____________\|___________________\|\n_____________79__________________59\n	212 -- 218	60 -- 66	-14.6837 kcal/mol	3.69927 kcal/mol	0.797083 kcal/mol	201 219@LB@ \| \|@LB@5'-AAG...GAAAA A A CCUAA...AAA-3'@LB@ UGGC AG UAUUUGGGU@LB@ \|\|\|\| \|\| \|\|\|\|:\|:\|\|@LB@ ACCG UC AUAAGCUCA@LB@3'-CGC...GUGCA AAA A ACUCU...AAG-5'@LB@ \| \|@LB@ 79 59@LB@@LB@@LB@Energy -10.19 kcal/mol@LB@Hybridization Energy -14.6837 kcal/mol@LB@Unfolding Energy - mRNA 3.69927 kcal/mol@LB@Unfolding Energy - sRNA 0.797083 kcal/mol@LB@@LB@Position - mRNA 202 -- 218@LB@Position - sRNA 60 -- 78@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 60 -- 66@LB@
138	0.02324	0.5385	b1826	mgrB	-8.64	0.179438	205 -- 238	60 -- 90	regulatory peptide for PhoPQ feedback inhibition	_____________204__________________________________239\n_____________\|____________________________________\|\n5'-UAC...AGUGA___________A___G_CGUUC__________U___GUUGG...AAU-3'\n______________AAAAGUUU_CG_UGG_U_____UGGUUGU_CG_GGU\n______________\|\|\|\|\|\|\|:_\|\|_\|\|\|_\|_____\|:\|\|\|:\|_\|\|_:\|\|\n______________UUUUCAAG_GC_ACC_A_____AUCAAUA_GC_UCA\n3'-CGC...AGGCG________U__A___G_A___________A______ACUCU...AAG-5'\n_____________\|____________________________________\|\n_____________91___________________________________59\n	226 -- 232	66 -- 72	-16.3224 kcal/mol	5.97183 kcal/mol	1.70935 kcal/mol	204 239@LB@ \| \|@LB@5'-UAC...AGUGA A G CGUUC U GUUGG...AAU-3'@LB@ AAAAGUUU CG UGG U UGGUUGU CG GGU@LB@ \|\|\|\|\|\|\|: \|\| \|\|\| \| \|:\|\|\|:\| \|\| :\|\|@LB@ UUUUCAAG GC ACC A AUCAAUA GC UCA@LB@3'-CGC...AGGCG U A G A A ACUCU...AAG-5'@LB@ \| \|@LB@ 91 59@LB@@LB@@LB@Energy -8.64 kcal/mol@LB@Hybridization Energy -16.3224 kcal/mol@LB@Unfolding Energy - mRNA 5.97183 kcal/mol@LB@Unfolding Energy - sRNA 1.70935 kcal/mol@LB@@LB@Position - mRNA 205 -- 238@LB@Position - sRNA 60 -- 90@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 66 -- 72@LB@
163	0.02879	0.5559	b4244	pyrI	-5.82	0.477897	276 -- 293	60 -- 77	aspartate carbamoyltransferase regulatory subunit	_____________275________________294\n_____________\|__________________\|\n5'-UUC...AGAUC_______AGCUG______CUGUUCA-3'\n______________GGUUUUA_____UUGAGU\n______________\|\|:\|\|\|\|_____\|:\|\|\|\|\n______________CCGAAAU_____AGCUCA\n3'-CGC...UGCAA_______CAAUA______ACUCU...AAG-5'\n_____________\|__________________\|\n_____________78_________________59\n	276 -- 282	71 -- 77	-12.7499 kcal/mol	6.13118 kcal/mol	0.796465 kcal/mol	275 294@LB@ \| \|@LB@5'-UUC...AGAUC AGCUG CUGUUCA-3'@LB@ GGUUUUA UUGAGU@LB@ \|\|:\|\|\|\| \|:\|\|\|\|@LB@ CCGAAAU AGCUCA@LB@3'-CGC...UGCAA CAAUA ACUCU...AAG-5'@LB@ \| \|@LB@ 78 59@LB@@LB@@LB@Energy -5.82 kcal/mol@LB@Hybridization Energy -12.7499 kcal/mol@LB@Unfolding Energy - mRNA 6.13118 kcal/mol@LB@Unfolding Energy - sRNA 0.796465 kcal/mol@LB@@LB@Position - mRNA 276 -- 293@LB@Position - sRNA 60 -- 77@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 71 -- 77@LB@
27	0.005053	0.5385	b2058	wcaB	-11.44	0.059229	168 -- 190	61 -- 82	putative acyl transferase	_____________167______________________191\n_____________\|________________________\|\n5'-ACC...GGCAA____C_____GA____________GGCGC...AGA-3'\n______________ACGU_UGGCU__UGG_UAUUCGGG\n______________\|\|\|\|_\|\|\|\|\|__\|:\|_\|\|\|\|\|\|:\|\n______________UGCA_ACCGA__AUC_AUAAGCUC\n3'-CGC...UCAAG__________A____A________AACUC...AAG-5'\n_____________\|________________________\|\n_____________83_______________________60\n	184 -- 190	61 -- 67	-21.3941 kcal/mol	8.91056 kcal/mol	1.03929 kcal/mol	167 191@LB@ \| \|@LB@5'-ACC...GGCAA C GA GGCGC...AGA-3'@LB@ ACGU UGGCU UGG UAUUCGGG@LB@ \|\|\|\| \|\|\|\|\| \|:\| \|\|\|\|\|\|:\|@LB@ UGCA ACCGA AUC AUAAGCUC@LB@3'-CGC...UCAAG A A AACUC...AAG-5'@LB@ \| \|@LB@ 83 60@LB@@LB@@LB@Energy -11.44 kcal/mol@LB@Hybridization Energy -21.3941 kcal/mol@LB@Unfolding Energy - mRNA 8.91056 kcal/mol@LB@Unfolding Energy - sRNA 1.03929 kcal/mol@LB@@LB@Position - mRNA 168 -- 190@LB@Position - sRNA 61 -- 82@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 61 -- 67@LB@
30	0.005373	0.5385	b1624	ydgJ	-10.76	0.078067	229 -- 247	61 -- 79	putative oxidoreductase	_____________228_________________248\n_____________\|___________________\|\n5'-GUA...GUUGA____G_A_______G____CAAAA...CGG-3'\n______________UUGG_U_UGGUUAU_CGAG\n______________\|\|\|\|_\|_\|:\|\|\|\|\|_\|\|\|\|\n______________AACC_A_AUCAAUA_GCUC\n3'-CGC...AGUGC____G_A_______A____AACUC...AAG-5'\n_____________\|___________________\|\n_____________80__________________60\n	236 -- 242	66 -- 72	-16.8363 kcal/mol	5.27817 kcal/mol	0.798019 kcal/mol	228 248@LB@ \| \|@LB@5'-GUA...GUUGA G A G CAAAA...CGG-3'@LB@ UUGG U UGGUUAU CGAG@LB@ \|\|\|\| \| \|:\|\|\|\|\| \|\|\|\|@LB@ AACC A AUCAAUA GCUC@LB@3'-CGC...AGUGC G A A AACUC...AAG-5'@LB@ \| \|@LB@ 80 60@LB@@LB@@LB@Energy -10.76 kcal/mol@LB@Hybridization Energy -16.8363 kcal/mol@LB@Unfolding Energy - mRNA 5.27817 kcal/mol@LB@Unfolding Energy - sRNA 0.798019 kcal/mol@LB@@LB@Position - mRNA 229 -- 247@LB@Position - sRNA 61 -- 79@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 66 -- 72@LB@
67	0.01284	0.5385	b1294	sapA	-9.42	0.132690	25 -- 48	61 -- 86	antimicrobial peptide transport ABC transporter periplasmic binding protein	_____________24_________________________49\n_____________\|__________________________\|\n5'-UAC...AAGUU________GA___A_______A____AAAUC...ACA-3'\n______________GUUC_UGU__GUU_UAGUUAU__GAG\n______________\|\|\|\|_:\|\|__\|:\|_\|\|\|\|\|\|\|__\|\|\|\n______________CAAG_GCA__CGA_AUCAAUA__CUC\n3'-CGC...GUUUU____U___AC___A_______AG___AACUC...AAG-5'\n_____________\|__________________________\|\n_____________87_________________________60\n	38 -- 44	66 -- 72	-17.3513 kcal/mol	6.21881 kcal/mol	1.70915 kcal/mol	24 49@LB@ \| \|@LB@5'-UAC...AAGUU GA A A AAAUC...ACA-3'@LB@ GUUC UGU GUU UAGUUAU GAG@LB@ \|\|\|\| :\|\| \|:\| \|\|\|\|\|\|\| \|\|\|@LB@ CAAG GCA CGA AUCAAUA CUC@LB@3'-CGC...GUUUU U AC A AG AACUC...AAG-5'@LB@ \| \|@LB@ 87 60@LB@@LB@@LB@Energy -9.42 kcal/mol@LB@Hybridization Energy -17.3513 kcal/mol@LB@Unfolding Energy - mRNA 6.21881 kcal/mol@LB@Unfolding Energy - sRNA 1.70915 kcal/mol@LB@@LB@Position - mRNA 25 -- 48@LB@Position - sRNA 61 -- 86@LB@Position Seed - mRNA 38 -- 44@LB@Position Seed - sRNA 66 -- 72@LB@
88	0.01545	0.5385	b3009	yghB	-9.13	0.148475	202 -- 216	61 -- 78	general envelope maintenance protein; DedA family inner membrane protein; putative multidrug efflux transporter	_____________201________________217\n_____________\|__________________\|\n5'-UCU...GUCCA_______________A__AUAUC...UUG-3'\n______________UGGCU___GUUAUUC_AG\n______________\|\|\|\|\|___\|\|\|\|\|\|\|_\|\|\n______________ACCGA___CAAUAAG_UC\n3'-CGC...GUGCA_____AAU_______C__AACUC...AAG-5'\n_____________\|__________________\|\n_____________79_________________60\n	207 -- 213	64 -- 70	-14.1767 kcal/mol	4.24529 kcal/mol	0.796888 kcal/mol	201 217@LB@ \| \|@LB@5'-UCU...GUCCA A AUAUC...UUG-3'@LB@ UGGCU GUUAUUC AG@LB@ \|\|\|\|\| \|\|\|\|\|\|\| \|\|@LB@ ACCGA CAAUAAG UC@LB@3'-CGC...GUGCA AAU C AACUC...AAG-5'@LB@ \| \|@LB@ 79 60@LB@@LB@@LB@Energy -9.13 kcal/mol@LB@Hybridization Energy -14.1767 kcal/mol@LB@Unfolding Energy - mRNA 4.24529 kcal/mol@LB@Unfolding Energy - sRNA 0.796888 kcal/mol@LB@@LB@Position - mRNA 202 -- 216@LB@Position - sRNA 61 -- 78@LB@Position Seed - mRNA 207 -- 213@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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