Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
57	0.002825	0.1597	b2233	yfaL	-10.30	0.013161	220 -- 233	34 -- 47	adhesin	_____________219____________234\n_____________\|______________\|\n5'-UAU...UCUAC______________UCUUU...CAU-3'\n______________GCAAGGAGUAUUUA\n______________\|\|\|\|\|:\|\|:\|:\|\|\|\n______________CGUUCUUCGUGAAU\n3'-UUU...GAAUU______________UUUUU...CAA-5'\n_____________\|______________\|\n_____________48_____________33\n	227 -- 233	34 -- 40	-18.4969 kcal/mol	2.11117 kcal/mol	6.08192 kcal/mol	219 234@LB@ \| \|@LB@5'-UAU...UCUAC UCUUU...CAU-3'@LB@ GCAAGGAGUAUUUA@LB@ \|\|\|\|\|:\|\|:\|:\|\|\|@LB@ CGUUCUUCGUGAAU@LB@3'-UUU...GAAUU UUUUU...CAA-5'@LB@ \| \|@LB@ 48 33@LB@@LB@@LB@Energy -10.30 kcal/mol@LB@Hybridization Energy -18.4969 kcal/mol@LB@Unfolding Energy - mRNA 2.11117 kcal/mol@LB@Unfolding Energy - sRNA 6.08192 kcal/mol@LB@@LB@Position - mRNA 220 -- 233@LB@Position - sRNA 34 -- 47@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 34 -- 40@LB@
107	0.009263	0.2693	b3034	nudF	-7.86	0.065629	202 -- 214	42 -- 54	ADP-ribose pyrophosphatase	_____________201___________215\n_____________\|_____________\|\n5'-AUU...AACAA_________C___CAACC...UUU-3'\n______________UGCUUAAGC_AGA\n______________\|\|\|\|\|\|\|\|\|_\|\|\|\n______________ACGAAUUCG_UCU\n3'-UUU...UUUGA_________U___UCGUG...CAA-5'\n_____________\|_____________\|\n_____________55____________41\n	204 -- 210	46 -- 52	-15.7149 kcal/mol	1.83586 kcal/mol	6.01534 kcal/mol	201 215@LB@ \| \|@LB@5'-AUU...AACAA C CAACC...UUU-3'@LB@ UGCUUAAGC AGA@LB@ \|\|\|\|\|\|\|\|\| \|\|\|@LB@ ACGAAUUCG UCU@LB@3'-UUU...UUUGA U UCGUG...CAA-5'@LB@ \| \|@LB@ 55 41@LB@@LB@@LB@Energy -7.86 kcal/mol@LB@Hybridization Energy -15.7149 kcal/mol@LB@Unfolding Energy - mRNA 1.83586 kcal/mol@LB@Unfolding Energy - sRNA 6.01534 kcal/mol@LB@@LB@Position - mRNA 202 -- 214@LB@Position - sRNA 42 -- 54@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 46 -- 52@LB@
165	0.01827	0.3566	b2937	speB	-7.30	0.092452	5 -- 22	25 -- 41	agmatinase	_____________4__________________23\n_____________\|__________________\|\n_______5'-CAAC___UC_____________AGGCA...CAG-3'\n______________AGU__CUUGAAGAGUUCG\n______________\|\|:__\|\|\|:\|\|:\|:\|\|\|\|\n______________UCG__GAAUUUUUUAAGC\n3'-UUU...GUUCU___U______________AAUGU...CAA-5'\n_____________\|__________________\|\n_____________42_________________24\n	16 -- 22	25 -- 31	-14.9284 kcal/mol	5.98061 kcal/mol	1.64839 kcal/mol	4 23@LB@ \| \|@LB@ 5'-CAAC UC AGGCA...CAG-3'@LB@ AGU CUUGAAGAGUUCG@LB@ \|\|: \|\|\|:\|\|:\|:\|\|\|\|@LB@ UCG GAAUUUUUUAAGC@LB@3'-UUU...GUUCU U AAUGU...CAA-5'@LB@ \| \|@LB@ 42 24@LB@@LB@@LB@Energy -7.30 kcal/mol@LB@Hybridization Energy -14.9284 kcal/mol@LB@Unfolding Energy - mRNA 5.98061 kcal/mol@LB@Unfolding Energy - sRNA 1.64839 kcal/mol@LB@@LB@Position - mRNA 5 -- 22@LB@Position - sRNA 25 -- 41@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 25 -- 31@LB@
103	0.00845	0.2642	b0936	ssuA	-4.91	0.333979	11 -- 31	10 -- 40	aliphatic sulfonate ABC transporter periplasmic binding protein	_____________10______________________________32\n_____________\|_______________________________\|\n5'-AGU...UAAGC_______________________________CUGCA...AUC-3'\n______________GCAC_UGAAA________GC_UCAGGAGAUC\n______________\|\|\|\|_\|:\|\|\|________:\|_:\|\|\|\|\|:\|\|\|\n______________CGUG_AUUUU________UG_GGUCCUUUAG\n3'-UUU...UUCUU____A_____UUAAGCAA__U__________ACUAC...CAA-5'\n_____________\|_______________________________\|\n_____________41______________________________9\n	25 -- 31	10 -- 16	-20.0893 kcal/mol	5.95403 kcal/mol	9.22048 kcal/mol	10 32@LB@ \| \|@LB@5'-AGU...UAAGC CUGCA...AUC-3'@LB@ GCAC UGAAA GC UCAGGAGAUC@LB@ \|\|\|\| \|:\|\|\| :\| :\|\|\|\|\|:\|\|\|@LB@ CGUG AUUUU UG GGUCCUUUAG@LB@3'-UUU...UUCUU A UUAAGCAA U ACUAC...CAA-5'@LB@ \| \|@LB@ 41 9@LB@@LB@@LB@Energy -4.91 kcal/mol@LB@Hybridization Energy -20.0893 kcal/mol@LB@Unfolding Energy - mRNA 5.95403 kcal/mol@LB@Unfolding Energy - sRNA 9.22048 kcal/mol@LB@@LB@Position - mRNA 11 -- 31@LB@Position - sRNA 10 -- 40@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 10 -- 16@LB@
154	0.01606	0.3359	b2587	kgtP	-4.55	0.394910	6 -- 12	52 -- 58	alpha-ketoglutarate transporter	_____________5_______13\n_____________\|_______\|\n______5'-UCCCC_______CCACU...UCG-3'\n______________AACUUGC\n______________\|\|\|\|\|\|\|\n______________UUGAACG\n3'-UUU...CUACU_______AAUUC...CAA-5'\n_____________\|_______\|\n_____________59______51\n	6 -- 12	52 -- 58	-7.82918 kcal/mol	0.15004 kcal/mol	3.13411 kcal/mol	5 13@LB@ \| \|@LB@ 5'-UCCCC CCACU...UCG-3'@LB@ AACUUGC@LB@ \|\|\|\|\|\|\|@LB@ UUGAACG@LB@3'-UUU...CUACU AAUUC...CAA-5'@LB@ \| \|@LB@ 59 51@LB@@LB@@LB@Energy -4.55 kcal/mol@LB@Hybridization Energy -7.82918 kcal/mol@LB@Unfolding Energy - mRNA 0.15004 kcal/mol@LB@Unfolding Energy - sRNA 3.13411 kcal/mol@LB@@LB@Position - mRNA 6 -- 12@LB@Position - sRNA 52 -- 58@LB@Position Seed - mRNA 6 -- 12@LB@Position Seed - sRNA 52 -- 58@LB@
106	0.009044	0.2693	b3360	pabA	-9.65	0.020637	134 -- 165	7 -- 41	aminodeoxychorismate synthase subunit II	_____________133_________________________________166\n_____________\|___________________________________\|\n5'-GCG...UAUUU____AAGUGGUAAG___AA________________GUAAA...CGU-3'\n______________AGCA___________CG____GCCGGGGAAUCUGA\n______________\|\|\|\|___________\|\|____:\|\|:\|\|:\|\|\|\|\|\|\|\n______________UCGU___________GC____UGGUCCUUUAGACU\n3'-UUU...GUUCU____GAAUUUUUUAA__AAUG______________ACACAA-5'\n_____________\|___________________________________\|\n_____________42__________________________________6\n	156 -- 162	10 -- 16	-26.3396 kcal/mol	7.46958 kcal/mol	9.22092 kcal/mol	133 166@LB@ \| \|@LB@5'-GCG...UAUUU AAGUGGUAAG AA GUAAA...CGU-3'@LB@ AGCA CG GCCGGGGAAUCUGA@LB@ \|\|\|\| \|\| :\|\|:\|\|:\|\|\|\|\|\|\|@LB@ UCGU GC UGGUCCUUUAGACU@LB@3'-UUU...GUUCU GAAUUUUUUAA AAUG ACACAA-5'@LB@ \| \|@LB@ 42 6@LB@@LB@@LB@Energy -9.65 kcal/mol@LB@Hybridization Energy -26.3396 kcal/mol@LB@Unfolding Energy - mRNA 7.46958 kcal/mol@LB@Unfolding Energy - sRNA 9.22092 kcal/mol@LB@@LB@Position - mRNA 134 -- 165@LB@Position - sRNA 7 -- 41@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 10 -- 16@LB@
180	0.02111	0.3768	b2753	iap	-4.77	0.357003	164 -- 179	25 -- 40	aminopeptidase in alkaline phosphatase isozyme conversion	_____________163______________180\n_____________\|________________\|\n5'-UAG...CUAUG___G_A__________CAUGG...CUA-3'\n______________GCG_U_AAAAAAUUUG\n______________\|\|:_\|_\|\|\|\|\|\|\|\|:\|\n______________CGU_A_UUUUUUAAGC\n3'-UUU...UUCUU___G_A__________AAUGU...CAA-5'\n_____________\|________________\|\n_____________41_______________24\n	170 -- 176	28 -- 34	-8.71545 kcal/mol	2.29678 kcal/mol	1.64821 kcal/mol	163 180@LB@ \| \|@LB@5'-UAG...CUAUG G A CAUGG...CUA-3'@LB@ GCG U AAAAAAUUUG@LB@ \|\|: \| \|\|\|\|\|\|\|\|:\|@LB@ CGU A UUUUUUAAGC@LB@3'-UUU...UUCUU G A AAUGU...CAA-5'@LB@ \| \|@LB@ 41 24@LB@@LB@@LB@Energy -4.77 kcal/mol@LB@Hybridization Energy -8.71545 kcal/mol@LB@Unfolding Energy - mRNA 2.29678 kcal/mol@LB@Unfolding Energy - sRNA 1.64821 kcal/mol@LB@@LB@Position - mRNA 164 -- 179@LB@Position - sRNA 25 -- 40@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 28 -- 34@LB@
17	0.0004446	0.08107	b1976	mtfA	-9.25	0.026966	241 -- 268	36 -- 59	anti-repressor for DgsA(Mlc)	_____________240___________________________269\n_____________\|_____________________________\|\n5'-AUA...ACAUC________CCUUCCCU_____________AUCGA...AAC-3'\n______________AAAC_UGC________GGCAGGAAGCACU\n______________\|\|\|\|_\|\|\|________:\|\|\|:\|\|\|\|\|\|\|\|\n______________UUUG_ACG________UCGUUCUUCGUGA\n3'-UUU...CCUAC____A___AAU__________________AUUUU...CAA-5'\n_____________\|_____________________________\|\n_____________60____________________________35\n	262 -- 268	36 -- 42	-23.9855 kcal/mol	8.48573 kcal/mol	6.24948 kcal/mol	240 269@LB@ \| \|@LB@5'-AUA...ACAUC CCUUCCCU AUCGA...AAC-3'@LB@ AAAC UGC GGCAGGAAGCACU@LB@ \|\|\|\| \|\|\| :\|\|\|:\|\|\|\|\|\|\|\|@LB@ UUUG ACG UCGUUCUUCGUGA@LB@3'-UUU...CCUAC A AAU AUUUU...CAA-5'@LB@ \| \|@LB@ 60 35@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -23.9855 kcal/mol@LB@Unfolding Energy - mRNA 8.48573 kcal/mol@LB@Unfolding Energy - sRNA 6.24948 kcal/mol@LB@@LB@Position - mRNA 241 -- 268@LB@Position - sRNA 36 -- 59@LB@Position Seed - mRNA 262 -- 268@LB@Position Seed - sRNA 36 -- 42@LB@
200	0.02417	0.3893	b1747	astA	-6.36	0.159223	49 -- 56	39 -- 46	arginine succinyltransferase	_____________48_______57\n_____________\|________\|\n5'-GGC...UCUCU________GGCGA...AAG-3'\n______________CAGGAAGC\n______________\|\|:\|\|\|\|\|\n______________GUUCUUCG\n3'-UUU...AAUUC________UGAAU...CAA-5'\n_____________\|________\|\n_____________47_______38\n	50 -- 56	39 -- 45	-10.5455 kcal/mol	1.56403 kcal/mol	2.62555 kcal/mol	48 57@LB@ \| \|@LB@5'-GGC...UCUCU GGCGA...AAG-3'@LB@ CAGGAAGC@LB@ \|\|:\|\|\|\|\|@LB@ GUUCUUCG@LB@3'-UUU...AAUUC UGAAU...CAA-5'@LB@ \| \|@LB@ 47 38@LB@@LB@@LB@Energy -6.36 kcal/mol@LB@Hybridization Energy -10.5455 kcal/mol@LB@Unfolding Energy - mRNA 1.56403 kcal/mol@LB@Unfolding Energy - sRNA 2.62555 kcal/mol@LB@@LB@Position - mRNA 49 -- 56@LB@Position - sRNA 39 -- 46@LB@Position Seed - mRNA 50 -- 56@LB@Position Seed - sRNA 39 -- 45@LB@
91	0.006547	0.2317	b1323	tyrR	-8.26	0.051378	202 -- 222	3 -- 23	aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase	_____________201___________________223\n_____________\|_____________________\|\n5'-UCG...UCCCA______U________UU____AAGAC...UUG-3'\n______________UGCGUC_GGAAGUCU__UGUG\n______________\|:\|::\|_\|\|\|\|:\|\|\|__\|\|\|\|\n______________AUGUGG_CCUUUAGA__ACAC\n3'-UUU...AAGCA______U________CU____AA-5'\n_____________\|_____________________\|\n_____________24____________________2\n	209 -- 215	10 -- 16	-19.6247 kcal/mol	3.79223 kcal/mol	7.5769 kcal/mol	201 223@LB@ \| \|@LB@5'-UCG...UCCCA U UU AAGAC...UUG-3'@LB@ UGCGUC GGAAGUCU UGUG@LB@ \|:\|::\| \|\|\|\|:\|\|\| \|\|\|\|@LB@ AUGUGG CCUUUAGA ACAC@LB@3'-UUU...AAGCA U CU AA-5'@LB@ \| \|@LB@ 24 2@LB@@LB@@LB@Energy -8.26 kcal/mol@LB@Hybridization Energy -19.6247 kcal/mol@LB@Unfolding Energy - mRNA 3.79223 kcal/mol@LB@Unfolding Energy - sRNA 7.5769 kcal/mol@LB@@LB@Position - mRNA 202 -- 222@LB@Position - sRNA 3 -- 23@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 10 -- 16@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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