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
44	0.009138	0.5385	b4148	sugE	-12.73	0.035076	273 -- 288	62 -- 77	multidrug efflux system protein	_____________272______________289\n_____________\|________________\|\n5'-CGC...CCCAC_________C______CGCCG...UUA-3'\n______________GGCUUUAGU_GUUUGA\n______________\|\|\|\|\|\|\|\|\|_:\|\|:\|\|\n______________CCGAAAUCA_UAAGCU\n3'-CGC...UGCAA_________A______CAACU...AAG-5'\n_____________\|________________\|\n_____________78_______________61\n	275 -- 281	69 -- 75	-18.0703 kcal/mol	4.60455 kcal/mol	0.736118 kcal/mol	272 289@LB@ \| \|@LB@5'-CGC...CCCAC C CGCCG...UUA-3'@LB@ GGCUUUAGU GUUUGA@LB@ \|\|\|\|\|\|\|\|\| :\|\|:\|\|@LB@ CCGAAAUCA UAAGCU@LB@3'-CGC...UGCAA A CAACU...AAG-5'@LB@ \| \|@LB@ 78 61@LB@@LB@@LB@Energy -12.73 kcal/mol@LB@Hybridization Energy -18.0703 kcal/mol@LB@Unfolding Energy - mRNA 4.60455 kcal/mol@LB@Unfolding Energy - sRNA 0.736118 kcal/mol@LB@@LB@Position - mRNA 273 -- 288@LB@Position - sRNA 62 -- 77@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 69 -- 75@LB@
33	0.006009	0.5385	b1264	trpE	-12.63	0.036478	39 -- 48	79 -- 88	component I of anthranilate synthase	_____________38_________49\n_____________\|__________\|\n5'-UGU...UACGC__________AAAAA...CGG-3'\n______________AAGUUCACGU\n______________\|\|\|\|\|\|\|\|\|\|\n______________UUCAAGUGCA\n3'-CGC...GCGUU__________ACCGA...AAG-5'\n_____________\|__________\|\n_____________89_________78\n	42 -- 48	79 -- 85	-13.8612 kcal/mol	0.721964 kcal/mol	0.505265 kcal/mol	38 49@LB@ \| \|@LB@5'-UGU...UACGC AAAAA...CGG-3'@LB@ AAGUUCACGU@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UUCAAGUGCA@LB@3'-CGC...GCGUU ACCGA...AAG-5'@LB@ \| \|@LB@ 89 78@LB@@LB@@LB@Energy -12.63 kcal/mol@LB@Hybridization Energy -13.8612 kcal/mol@LB@Unfolding Energy - mRNA 0.721964 kcal/mol@LB@Unfolding Energy - sRNA 0.505265 kcal/mol@LB@@LB@Position - mRNA 39 -- 48@LB@Position - sRNA 79 -- 88@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 79 -- 85@LB@
145	0.02443	0.5467	b2569	lepA	-12.53	0.038132	5 -- 17	71 -- 85	back-translocating elongation factor EF4 GTPase	_____________4_______________18\n_____________\|_______________\|\n_______5'-UGAU_______________UUGCA...ACC-3'\n______________UUCAC__UGGCUUUG\n______________\|\|\|\|\|__\|\|\|\|\|\|\|:\n______________AAGUG__ACCGAAAU\n3'-CGC...UUUUC_____CA________CAAUA...AAG-5'\n_____________\|_______________\|\n_____________86______________70\n	11 -- 17	71 -- 77	-14.3569 kcal/mol	1.27074 kcal/mol	0.560731 kcal/mol	4 18@LB@ \| \|@LB@ 5'-UGAU UUGCA...ACC-3'@LB@ UUCAC UGGCUUUG@LB@ \|\|\|\|\| \|\|\|\|\|\|\|:@LB@ AAGUG ACCGAAAU@LB@3'-CGC...UUUUC CA CAAUA...AAG-5'@LB@ \| \|@LB@ 86 70@LB@@LB@@LB@Energy -12.53 kcal/mol@LB@Hybridization Energy -14.3569 kcal/mol@LB@Unfolding Energy - mRNA 1.27074 kcal/mol@LB@Unfolding Energy - sRNA 0.560731 kcal/mol@LB@@LB@Position - mRNA 5 -- 17@LB@Position - sRNA 71 -- 85@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 71 -- 77@LB@
5	0.0009313	0.5385	b3829	metE	-12.51	0.038445	233 -- 242	75 -- 84	5-methyltetrahydropteroyltriglutamate- homocysteine S-methyltransferase	_____________232________243\n_____________\|__________\|\n5'-GAG...UUCCC__________CUGCG...GUG-3'\n______________UCGCGUUGGC\n______________\|\|:\|\|\|\|\|\|\|\n______________AGUGCAACCG\n3'-CGC...UUUCA__________AAAUC...AAG-5'\n_____________\|__________\|\n_____________85_________74\n	236 -- 242	75 -- 81	-17.7887 kcal/mol	4.77726 kcal/mol	0.505918 kcal/mol	232 243@LB@ \| \|@LB@5'-GAG...UUCCC CUGCG...GUG-3'@LB@ UCGCGUUGGC@LB@ \|\|:\|\|\|\|\|\|\|@LB@ AGUGCAACCG@LB@3'-CGC...UUUCA AAAUC...AAG-5'@LB@ \| \|@LB@ 85 74@LB@@LB@@LB@Energy -12.51 kcal/mol@LB@Hybridization Energy -17.7887 kcal/mol@LB@Unfolding Energy - mRNA 4.77726 kcal/mol@LB@Unfolding Energy - sRNA 0.505918 kcal/mol@LB@@LB@Position - mRNA 233 -- 242@LB@Position - sRNA 75 -- 84@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 75 -- 81@LB@
34	0.00612	0.5385	b1837	yebW	-12.39	0.040382	203 -- 226	63 -- 86	uncharacterized protein	_____________202______________________227\n_____________\|________________________\|\n5'-ACC...GAAAU_______C____ACUUU_______CUACC...UGA-3'\n______________GUUCGCG_UGGU_____UUGUUUG\n______________\|\|\|\|:\|\|_\|\|\|:_____\|\|:\|\|:\|\n______________CAAGUGC_ACCG_____AAUAAGC\n3'-CGC...GUUUU_______A____AAAUC_______UCAAC...AAG-5'\n_____________\|________________________\|\n_____________87_______________________62\n	220 -- 226	63 -- 69	-18.9836 kcal/mol	4.90011 kcal/mol	1.69827 kcal/mol	202 227@LB@ \| \|@LB@5'-ACC...GAAAU C ACUUU CUACC...UGA-3'@LB@ GUUCGCG UGGU UUGUUUG@LB@ \|\|\|\|:\|\| \|\|\|: \|\|:\|\|:\|@LB@ CAAGUGC ACCG AAUAAGC@LB@3'-CGC...GUUUU A AAAUC UCAAC...AAG-5'@LB@ \| \|@LB@ 87 62@LB@@LB@@LB@Energy -12.39 kcal/mol@LB@Hybridization Energy -18.9836 kcal/mol@LB@Unfolding Energy - mRNA 4.90011 kcal/mol@LB@Unfolding Energy - sRNA 1.69827 kcal/mol@LB@@LB@Position - mRNA 203 -- 226@LB@Position - sRNA 63 -- 86@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 63 -- 69@LB@
35	0.006586	0.5385	b2351	gtrB	-12.36	0.040837	174 -- 213	48 -- 89	CPS-53 (KpLE1) prophage; bactoprenol glucosyl transferase	_____________173________________________________________214\n_____________\|__________________________________________\|\n5'-GCA...UAUUC_____________U______GG__G___AA___A__UA____UUGUA...AAG-3'\n______________AAAGUUCAU__UG_CUUUAG__AU_CGA__UGA_GA__UCUC\n______________\|\|\|\|\|\|\|\|:__\|\|_\|\|\|\|\|\|__\|\|_\|\|\|__\|\|\|_:\|__\|\|\|\|\n______________UUUCAAGUG__AC_GAAAUC__UA_GCU__ACU_UU__AGAG\n3'-CGC...GGCGU_________CA__C______AA__A___CA___C__UG____CUUUG...AAG-5'\n_____________\|__________________________________________\|\n_____________90_________________________________________47\n	176 -- 182	81 -- 87	-27.281 kcal/mol	10.5075 kcal/mol	4.41572 kcal/mol	173 214@LB@ \| \|@LB@5'-GCA...UAUUC U GG G AA A UA UUGUA...AAG-3'@LB@ AAAGUUCAU UG CUUUAG AU CGA UGA GA UCUC@LB@ \|\|\|\|\|\|\|\|: \|\| \|\|\|\|\|\| \|\| \|\|\| \|\|\| :\| \|\|\|\|@LB@ UUUCAAGUG AC GAAAUC UA GCU ACU UU AGAG@LB@3'-CGC...GGCGU CA C AA A CA C UG CUUUG...AAG-5'@LB@ \| \|@LB@ 90 47@LB@@LB@@LB@Energy -12.36 kcal/mol@LB@Hybridization Energy -27.281 kcal/mol@LB@Unfolding Energy - mRNA 10.5075 kcal/mol@LB@Unfolding Energy - sRNA 4.41572 kcal/mol@LB@@LB@Position - mRNA 174 -- 213@LB@Position - sRNA 48 -- 89@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 81 -- 87@LB@
73	0.0135	0.5385	b3362	yhfG	-12.23	0.043008	184 -- 212	50 -- 86	putative antitoxin for Fic	_____________183___________________________________213\n_____________\|_____________________________________\|\n5'-GAU...GACAC_____G_GA___A__________A___GA________ACCGA...CUU-3'\n______________GUUCA_G__GGC_________UC_AGU__AGAAACUC\n______________\|\|\|\|\|_\|__\|\|\|_________\|\|_\|\|\|__\|\|\|\|\|\|\|\|\n______________CAAGU_C__CCG_________AG_UCA__UCUUUGAG\n3'-CGC...GUUUU_____G_AA___AAAUCAAUA__C___AC________AGCUU...AAG-5'\n_____________\|_____________________________________\|\n_____________87____________________________________49\n	206 -- 212	50 -- 56	-25.6976 kcal/mol	9.05881 kcal/mol	4.40785 kcal/mol	183 213@LB@ \| \|@LB@5'-GAU...GACAC G GA A A GA ACCGA...CUU-3'@LB@ GUUCA G GGC UC AGU AGAAACUC@LB@ \|\|\|\|\| \| \|\|\| \|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ CAAGU C CCG AG UCA UCUUUGAG@LB@3'-CGC...GUUUU G AA AAAUCAAUA C AC AGCUU...AAG-5'@LB@ \| \|@LB@ 87 49@LB@@LB@@LB@Energy -12.23 kcal/mol@LB@Hybridization Energy -25.6976 kcal/mol@LB@Unfolding Energy - mRNA 9.05881 kcal/mol@LB@Unfolding Energy - sRNA 4.40785 kcal/mol@LB@@LB@Position - mRNA 184 -- 212@LB@Position - sRNA 50 -- 86@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 50 -- 56@LB@
98	0.0165	0.5385	b0151	fhuC	-12.15	0.044517	184 -- 202	66 -- 85	iron(3+)-hydroxamate import ABC transporter ATPase	_____________183____________________203\n_____________\|______________________\|\n5'-CUG...CCCAU_____AA_______________GCAGG...CCU-3'\n______________UUCAC__GUUGGCU___GUUAU\n______________\|\|\|\|\|__\|\|\|\|\|\|\|___\|\|\|\|\|\n______________AAGUG__CAACCGA___CAAUA\n3'-CGC...UUUUC______________AAU_____AGCUC...AAG-5'\n_____________\|______________________\|\n_____________86_____________________65\n	191 -- 197	74 -- 80	-16.912 kcal/mol	4.1925 kcal/mol	0.573112 kcal/mol	183 203@LB@ \| \|@LB@5'-CUG...CCCAU AA GCAGG...CCU-3'@LB@ UUCAC GUUGGCU GUUAU@LB@ \|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ AAGUG CAACCGA CAAUA@LB@3'-CGC...UUUUC AAU AGCUC...AAG-5'@LB@ \| \|@LB@ 86 65@LB@@LB@@LB@Energy -12.15 kcal/mol@LB@Hybridization Energy -16.912 kcal/mol@LB@Unfolding Energy - mRNA 4.1925 kcal/mol@LB@Unfolding Energy - sRNA 0.573112 kcal/mol@LB@@LB@Position - mRNA 184 -- 202@LB@Position - sRNA 66 -- 85@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 74 -- 80@LB@
70	0.01301	0.5385	b1424	opgD	-12.13	0.044753	222 -- 240	70 -- 90	OPG biosynthetic periplasmic protein	_____________221___________________241\n_____________\|_____________________\|\n5'-AAU...UUAUU_________A_______A___CCGCC...CAG-3'\n______________AAAGGUUCA___UGGCU_UGG\n______________\|\|\|:\|\|\|\|\|___\|\|\|\|\|_\|:\|\n______________UUUUCAAGU___ACCGA_AUC\n3'-CGC...AGGCG_________GCA_____A___AAUAA...AAG-5'\n_____________\|_____________________\|\n_____________91____________________69\n	224 -- 230	82 -- 88	-16.4191 kcal/mol	3.71348 kcal/mol	0.572228 kcal/mol	221 241@LB@ \| \|@LB@5'-AAU...UUAUU A A CCGCC...CAG-3'@LB@ AAAGGUUCA UGGCU UGG@LB@ \|\|\|:\|\|\|\|\| \|\|\|\|\| \|:\|@LB@ UUUUCAAGU ACCGA AUC@LB@3'-CGC...AGGCG GCA A AAUAA...AAG-5'@LB@ \| \|@LB@ 91 69@LB@@LB@@LB@Energy -12.13 kcal/mol@LB@Hybridization Energy -16.4191 kcal/mol@LB@Unfolding Energy - mRNA 3.71348 kcal/mol@LB@Unfolding Energy - sRNA 0.572228 kcal/mol@LB@@LB@Position - mRNA 222 -- 240@LB@Position - sRNA 70 -- 90@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 82 -- 88@LB@
19	0.003195	0.5385	b3739	atpI	-12.12	0.045044	59 -- 85	62 -- 85	ATP synthase membrane-bound accessory factor	_____________58___________________________86\n_____________\|____________________________\|\n5'-GAA...AUUUA_____CUU______AC____________AAUCA...ACC-3'\n______________UUCAC___UUGGCU__UUA_UUGUUUGA\n______________\|\|\|\|\|___\|\|\|\|\|\|__\|\|\|_\|\|:\|\|:\|\|\n______________AAGUG___AACCGA__AAU_AAUAAGCU\n3'-CGC...UUUUC_____C_____________C________CAACU...AAG-5'\n_____________\|____________________________\|\n_____________86___________________________61\n	79 -- 85	62 -- 68	-17.7596 kcal/mol	3.93623 kcal/mol	1.70582 kcal/mol	58 86@LB@ \| \|@LB@5'-GAA...AUUUA CUU AC AAUCA...ACC-3'@LB@ UUCAC UUGGCU UUA UUGUUUGA@LB@ \|\|\|\|\| \|\|\|\|\|\| \|\|\| \|\|:\|\|:\|\|@LB@ AAGUG AACCGA AAU AAUAAGCU@LB@3'-CGC...UUUUC C C CAACU...AAG-5'@LB@ \| \|@LB@ 86 61@LB@@LB@@LB@Energy -12.12 kcal/mol@LB@Hybridization Energy -17.7596 kcal/mol@LB@Unfolding Energy - mRNA 3.93623 kcal/mol@LB@Unfolding Energy - sRNA 1.70582 kcal/mol@LB@@LB@Position - mRNA 59 -- 85@LB@Position - sRNA 62 -- 85@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 62 -- 68@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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