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
29	0.000834	0.09021	b2798	ygdG	-11.41	0.005967	211 -- 245	24 -- 57	Ssb-binding protein misidentified as ExoIX	_____________210_________________________________246\n_____________\|___________________________________\|\n5'-CCA...UGUUC_________UUGUC__U_____GAAUCUU______CGCAU...UCG-3'\n______________AUUUGCUUA_____GA_GCACU_______AUUCGU\n______________\|:\|\|\|\|\|\|\|_____\|\|_\|\|\|\|\|_______\|\|\|\|\|\|\n______________UGAACGAAU_____CU_CGUGA_______UAAGCA\n3'-UUU...UACUU_________UCGUU__U_____AUUUUU_______AUGUG...CAA-5'\n_____________\|___________________________________\|\n_____________58__________________________________23\n	213 -- 219	49 -- 55	-23.2646 kcal/mol	5.57825 kcal/mol	6.27607 kcal/mol	210 246@LB@ \| \|@LB@5'-CCA...UGUUC UUGUC U GAAUCUU CGCAU...UCG-3'@LB@ AUUUGCUUA GA GCACU AUUCGU@LB@ \|:\|\|\|\|\|\|\| \|\| \|\|\|\|\| \|\|\|\|\|\|@LB@ UGAACGAAU CU CGUGA UAAGCA@LB@3'-UUU...UACUU UCGUU U AUUUUU AUGUG...CAA-5'@LB@ \| \|@LB@ 58 23@LB@@LB@@LB@Energy -11.41 kcal/mol@LB@Hybridization Energy -23.2646 kcal/mol@LB@Unfolding Energy - mRNA 5.57825 kcal/mol@LB@Unfolding Energy - sRNA 6.27607 kcal/mol@LB@@LB@Position - mRNA 211 -- 245@LB@Position - sRNA 24 -- 57@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 49 -- 55@LB@
49	0.002267	0.1465	b0592	fepB	-6.35	0.159662	143 -- 160	24 -- 40	ferrienterobactin ABC transporter periplasmic binding protein	_____________142________________161\n_____________\|__________________\|\n5'-AUA...AUUGU______UGUC________CAUUA...UUA-3'\n______________GCGCUU____GAAUUUGU\n______________\|\|:\|\|\|____:\|\|\|\|:\|\|\n______________CGUGAA____UUUAAGCA\n3'-UUU...UUCUU______UUU_________AUGUG...CAA-5'\n_____________\|__________________\|\n_____________41_________________23\n	154 -- 160	24 -- 30	-12.773 kcal/mol	4.77335 kcal/mol	1.64869 kcal/mol	142 161@LB@ \| \|@LB@5'-AUA...AUUGU UGUC CAUUA...UUA-3'@LB@ GCGCUU GAAUUUGU@LB@ \|\|:\|\|\| :\|\|\|\|:\|\|@LB@ CGUGAA UUUAAGCA@LB@3'-UUU...UUCUU UUU AUGUG...CAA-5'@LB@ \| \|@LB@ 41 23@LB@@LB@@LB@Energy -6.35 kcal/mol@LB@Hybridization Energy -12.773 kcal/mol@LB@Unfolding Energy - mRNA 4.77335 kcal/mol@LB@Unfolding Energy - sRNA 1.64869 kcal/mol@LB@@LB@Position - mRNA 143 -- 160@LB@Position - sRNA 24 -- 40@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 24 -- 30@LB@
56	0.002803	0.1597	b2514	hisS	-5.93	0.201249	279 -- 295	24 -- 41	histidyl tRNA synthetase	_____________278_________________296\n_____________\|___________________\|\n5'-AUG...UUGAA_____AC____________GCUCG-3'\n______________GGCAC__UGAAAAA__CGU\n______________:\|\|\|\|__\|:\|\|\|\|\|__\|\|\|\n______________UCGUG__AUUUUUU__GCA\n3'-UUU...GUUCU_____A________AA___AUGUG...CAA-5'\n_____________\|___________________\|\n_____________42__________________23\n	286 -- 292	29 -- 35	-10.1195 kcal/mol	2.54562 kcal/mol	1.64881 kcal/mol	278 296@LB@ \| \|@LB@5'-AUG...UUGAA AC GCUCG-3'@LB@ GGCAC UGAAAAA CGU@LB@ :\|\|\|\| \|:\|\|\|\|\| \|\|\|@LB@ UCGUG AUUUUUU GCA@LB@3'-UUU...GUUCU A AA AUGUG...CAA-5'@LB@ \| \|@LB@ 42 23@LB@@LB@@LB@Energy -5.93 kcal/mol@LB@Hybridization Energy -10.1195 kcal/mol@LB@Unfolding Energy - mRNA 2.54562 kcal/mol@LB@Unfolding Energy - sRNA 1.64881 kcal/mol@LB@@LB@Position - mRNA 279 -- 295@LB@Position - sRNA 24 -- 41@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 29 -- 35@LB@
111	0.009564	0.2693	b2040	rfbD	-5.00	0.321114	87 -- 99	24 -- 42	dTDP-L-rhamnose synthase NAD(P)-dependent dTDP-4-dehydrorhamnose reductase subunit	_____________86__________________100\n_____________\|___________________\|\n5'-GAU...UUUGA___________________AAAAC...CUA-3'\n______________GAGCG______GGAUUCGU\n______________:\|\|\|:______::\|\|\|\|\|\|\n______________UUCGU______UUUAAGCA\n3'-UUU...CGUUC_____GAAUUU________AUGUG...CAA-5'\n_____________\|___________________\|\n_____________43__________________23\n	93 -- 99	24 -- 30	-9.51502 kcal/mol	2.86783 kcal/mol	1.64896 kcal/mol	86 100@LB@ \| \|@LB@5'-GAU...UUUGA AAAAC...CUA-3'@LB@ GAGCG GGAUUCGU@LB@ :\|\|\|: ::\|\|\|\|\|\|@LB@ UUCGU UUUAAGCA@LB@3'-UUU...CGUUC GAAUUU AUGUG...CAA-5'@LB@ \| \|@LB@ 43 23@LB@@LB@@LB@Energy -5.00 kcal/mol@LB@Hybridization Energy -9.51502 kcal/mol@LB@Unfolding Energy - mRNA 2.86783 kcal/mol@LB@Unfolding Energy - sRNA 1.64896 kcal/mol@LB@@LB@Position - mRNA 87 -- 99@LB@Position - sRNA 24 -- 42@LB@Position Seed - mRNA 93 -- 99@LB@Position Seed - sRNA 24 -- 30@LB@
124	0.01089	0.2829	b0186	ldcC	-10.51	0.011388	34 -- 66	24 -- 58	lysine decarboxylase 2 constitutive	_____________33___________________________________67\n_____________\|____________________________________\|\n5'-AAA...AUCUC___G__________CU____________________CGUUA...UUA-3'\n______________GAC_UG_UUAAGCA__GAAG_AUUUAAAAAA_UCGU\n______________:\|\|_\|\|_\|\|\|\|\|\|\|__\|\|\|\|_\|:\|\|\|\|\|\|\|\|_\|\|\|\|\n______________UUG_AC_AAUUCGU__CUUC_UGAAUUUUUU_AGCA\n3'-UUU...CUACU___A__G_______U_____G__________A____AUGUG...CAA-5'\n_____________\|____________________________________\|\n_____________59___________________________________23\n	53 -- 59	32 -- 38	-24.2219 kcal/mol	7.43557 kcal/mol	6.27608 kcal/mol	33 67@LB@ \| \|@LB@5'-AAA...AUCUC G CU CGUUA...UUA-3'@LB@ GAC UG UUAAGCA GAAG AUUUAAAAAA UCGU@LB@ :\|\| \|\| \|\|\|\|\|\|\| \|\|\|\| \|:\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UUG AC AAUUCGU CUUC UGAAUUUUUU AGCA@LB@3'-UUU...CUACU A G U G A AUGUG...CAA-5'@LB@ \| \|@LB@ 59 23@LB@@LB@@LB@Energy -10.51 kcal/mol@LB@Hybridization Energy -24.2219 kcal/mol@LB@Unfolding Energy - mRNA 7.43557 kcal/mol@LB@Unfolding Energy - sRNA 6.27608 kcal/mol@LB@@LB@Position - mRNA 34 -- 66@LB@Position - sRNA 24 -- 58@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 32 -- 38@LB@
128	0.01225	0.3033	b3299	rpmJ	-5.94	0.199813	193 -- 212	24 -- 42	50S ribosomal subunit protein L36	_____________192__________________213\n_____________\|____________________\|\n5'-GGA...ACGGA_____AAAAU__________GCUUC...AUA-3'\n______________GAGUA_____GAAAGUUCGU\n______________:\|\|:\|_____:\|\|\|:\|\|\|\|\|\n______________UUCGU_____UUUUUAAGCA\n3'-UUU...CGUUC_____GAAU___________AUGUG...CAA-5'\n_____________\|____________________\|\n_____________43___________________23\n	206 -- 212	24 -- 30	-12.4383 kcal/mol	4.85088 kcal/mol	1.64896 kcal/mol	192 213@LB@ \| \|@LB@5'-GGA...ACGGA AAAAU GCUUC...AUA-3'@LB@ GAGUA GAAAGUUCGU@LB@ :\|\|:\| :\|\|\|:\|\|\|\|\|@LB@ UUCGU UUUUUAAGCA@LB@3'-UUU...CGUUC GAAU AUGUG...CAA-5'@LB@ \| \|@LB@ 43 23@LB@@LB@@LB@Energy -5.94 kcal/mol@LB@Hybridization Energy -12.4383 kcal/mol@LB@Unfolding Energy - mRNA 4.85088 kcal/mol@LB@Unfolding Energy - sRNA 1.64896 kcal/mol@LB@@LB@Position - mRNA 193 -- 212@LB@Position - sRNA 24 -- 42@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 24 -- 30@LB@
138	0.01322	0.3087	b1523	yneG	-4.22	0.452951	267 -- 281	24 -- 41	DUF4186 family protein	_____________266________________282\n_____________\|__________________\|\n5'-AUG...GUCUG_____________G____CAGUA...AAG-3'\n______________GGCA__UGAAAGA__CGU\n______________:\|\|\|__\|:\|\|\|:\|__\|\|\|\n______________UCGU__AUUUUUU__GCA\n3'-UUU...GUUCU____GA_______AA___AUGUG...CAA-5'\n_____________\|__________________\|\n_____________42_________________23\n	271 -- 277	29 -- 35	-8.58312 kcal/mol	2.71204 kcal/mol	1.64881 kcal/mol	266 282@LB@ \| \|@LB@5'-AUG...GUCUG G CAGUA...AAG-3'@LB@ GGCA UGAAAGA CGU@LB@ :\|\|\| \|:\|\|\|:\| \|\|\|@LB@ UCGU AUUUUUU GCA@LB@3'-UUU...GUUCU GA AA AUGUG...CAA-5'@LB@ \| \|@LB@ 42 23@LB@@LB@@LB@Energy -4.22 kcal/mol@LB@Hybridization Energy -8.58312 kcal/mol@LB@Unfolding Energy - mRNA 2.71204 kcal/mol@LB@Unfolding Energy - sRNA 1.64881 kcal/mol@LB@@LB@Position - mRNA 267 -- 281@LB@Position - sRNA 24 -- 41@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 29 -- 35@LB@
147	0.01475	0.3231	b0084	ftsI	-4.75	0.360226	157 -- 172	24 -- 39	transpeptidase involved in septal peptidoglycan synthesis; penicillin-binding protein 3	_____________156_______________173\n_____________\|_________________\|\n5'-GUU...UCCGU___A________A____AGUGC...UGG-3'\n______________CAC__AGAAAAU_UCGU\n______________\|\|\|__\|:\|\|\|\|\|_\|\|\|\|\n______________GUG__UUUUUUA_AGCA\n3'-UUU...UCUUC___AA____________AUGUG...CAA-5'\n_____________\|_________________\|\n_____________40________________23\n	161 -- 167	28 -- 34	-7.76704 kcal/mol	1.36905 kcal/mol	1.64726 kcal/mol	156 173@LB@ \| \|@LB@5'-GUU...UCCGU A A AGUGC...UGG-3'@LB@ CAC AGAAAAU UCGU@LB@ \|\|\| \|:\|\|\|\|\| \|\|\|\|@LB@ GUG UUUUUUA AGCA@LB@3'-UUU...UCUUC AA AUGUG...CAA-5'@LB@ \| \|@LB@ 40 23@LB@@LB@@LB@Energy -4.75 kcal/mol@LB@Hybridization Energy -7.76704 kcal/mol@LB@Unfolding Energy - mRNA 1.36905 kcal/mol@LB@Unfolding Energy - sRNA 1.64726 kcal/mol@LB@@LB@Position - mRNA 157 -- 172@LB@Position - sRNA 24 -- 39@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 28 -- 34@LB@
176	0.02022	0.37	b0495	ybbA	-5.55	0.244939	212 -- 247	24 -- 59	putative ABC transporter ATPase	_____________211___________________________________248\n_____________\|_____________________________________\|\n5'-GCC...GCGGA____A_____G____UCAUCAU___________C___CGGUC...UCA-3'\n______________AAAC_UUGUU_AAGU________CUUAAGAAGU_CGU\n______________\|\|\|\|_\|\|\|:\|_\|\|\|:________\|\|\|\|\|:\|\|:\|_\|\|\|\n______________UUUG_AACGA_UUCG________GAAUUUUUUA_GCA\n3'-UUU...CCUAC__________A____UUCUUCGU__________A___AUGUG...CAA-5'\n_____________\|_____________________________________\|\n_____________60____________________________________23\n	235 -- 241	30 -- 36	-18.4731 kcal/mol	6.64875 kcal/mol	6.27609 kcal/mol	211 248@LB@ \| \|@LB@5'-GCC...GCGGA A G UCAUCAU C CGGUC...UCA-3'@LB@ AAAC UUGUU AAGU CUUAAGAAGU CGU@LB@ \|\|\|\| \|\|\|:\| \|\|\|: \|\|\|\|\|:\|\|:\| \|\|\|@LB@ UUUG AACGA UUCG GAAUUUUUUA GCA@LB@3'-UUU...CCUAC A UUCUUCGU A AUGUG...CAA-5'@LB@ \| \|@LB@ 60 23@LB@@LB@@LB@Energy -5.55 kcal/mol@LB@Hybridization Energy -18.4731 kcal/mol@LB@Unfolding Energy - mRNA 6.64875 kcal/mol@LB@Unfolding Energy - sRNA 6.27609 kcal/mol@LB@@LB@Position - mRNA 212 -- 247@LB@Position - sRNA 24 -- 59@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 30 -- 36@LB@
190	0.02239	0.3796	b0724	sdhB	-6.89	0.117799	143 -- 176	24 -- 60	succinate dehydrogenase FeS subunit	_____________142____________________________________177\n_____________\|______________________________________\|\n5'-UUU...GAACC_________GCCC____UUCC____C____________ACUUA...UGA-3'\n______________GAAAC_UGC____GGCA_____CGC___GAAGAUUCGU\n______________\|\|\|\|\|_\|\|\|____:\|\|\|_____\|:\|___:\|\|:\|\|\|\|\|\|\n______________CUUUG_ACG____UCGU_____GUG___UUUUUAAGCA\n3'-UUU...CCCUA_____A___AAU_____UCUUC___AAU__________AUGUG...CAA-5'\n_____________\|______________________________________\|\n_____________61_____________________________________23\n	170 -- 176	24 -- 30	-22.9017 kcal/mol	9.73835 kcal/mol	6.27609 kcal/mol	142 177@LB@ \| \|@LB@5'-UUU...GAACC GCCC UUCC C ACUUA...UGA-3'@LB@ GAAAC UGC GGCA CGC GAAGAUUCGU@LB@ \|\|\|\|\| \|\|\| :\|\|\| \|:\| :\|\|:\|\|\|\|\|\|@LB@ CUUUG ACG UCGU GUG UUUUUAAGCA@LB@3'-UUU...CCCUA A AAU UCUUC AAU AUGUG...CAA-5'@LB@ \| \|@LB@ 61 23@LB@@LB@@LB@Energy -6.89 kcal/mol@LB@Hybridization Energy -22.9017 kcal/mol@LB@Unfolding Energy - mRNA 9.73835 kcal/mol@LB@Unfolding Energy - sRNA 6.27609 kcal/mol@LB@@LB@Position - mRNA 143 -- 176@LB@Position - sRNA 24 -- 60@LB@Position Seed - mRNA 170 -- 176@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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service.

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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