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
84	0.005596	0.2146	b4065	yjcE	-5.39	0.265673	197 -- 210	9 -- 22	putative cation/proton antiporter	_____________196____________211\n_____________\|______________\|\n5'-UAU...AGGGA____AU________UCUUC...UGC-3'\n______________ACGC__GGAAAUCU\n______________\|\|:\|__\|\|\|\|\|\|\|\|\n______________UGUG__CCUUUAGA\n3'-UUU...AGCAA____GU________CUACACAA-5'\n_____________\|______________\|\n_____________23_____________8\n	203 -- 209	10 -- 16	-15.8377 kcal/mol	2.89158 kcal/mol	7.5588 kcal/mol	196 211@LB@ \| \|@LB@5'-UAU...AGGGA AU UCUUC...UGC-3'@LB@ ACGC GGAAAUCU@LB@ \|\|:\| \|\|\|\|\|\|\|\|@LB@ UGUG CCUUUAGA@LB@3'-UUU...AGCAA GU CUACACAA-5'@LB@ \| \|@LB@ 23 8@LB@@LB@@LB@Energy -5.39 kcal/mol@LB@Hybridization Energy -15.8377 kcal/mol@LB@Unfolding Energy - mRNA 2.89158 kcal/mol@LB@Unfolding Energy - sRNA 7.5588 kcal/mol@LB@@LB@Position - mRNA 197 -- 210@LB@Position - sRNA 9 -- 22@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 10 -- 16@LB@
8	5.642e-05	0.02272	b2282	nuoH	-5.33	0.272754	189 -- 221	13 -- 44	NADH:ubiquinone oxidoreductase membrane subunit H	_____________188________________________________222\n_____________\|__________________________________\|\n5'-CUC...CUCAA________AACAAU_____G_A__U_________CUGAU...GCU-3'\n______________GGAGGCAC______GAGUU_G_UA_CACC_GGAA\n______________:\|\|:\|\|\|\|______:\|:\|\|_\|_\|\|_\|\|\|\|_\|\|\|\|\n______________UCUUCGUG______UUUAA_C_AU_GUGG_CCUU\n3'-UUU...UUCGU________AAUUU______G_A_______U____UAGAC...CAA-5'\n_____________\|__________________________________\|\n_____________45_________________________________12\n	190 -- 196	37 -- 43	-24.1154 kcal/mol	6.60325 kcal/mol	12.1776 kcal/mol	188 222@LB@ \| \|@LB@5'-CUC...CUCAA AACAAU G A U CUGAU...GCU-3'@LB@ GGAGGCAC GAGUU G UA CACC GGAA@LB@ :\|\|:\|\|\|\| :\|:\|\| \| \|\| \|\|\|\| \|\|\|\|@LB@ UCUUCGUG UUUAA C AU GUGG CCUU@LB@3'-UUU...UUCGU AAUUU G A U UAGAC...CAA-5'@LB@ \| \|@LB@ 45 12@LB@@LB@@LB@Energy -5.33 kcal/mol@LB@Hybridization Energy -24.1154 kcal/mol@LB@Unfolding Energy - mRNA 6.60325 kcal/mol@LB@Unfolding Energy - sRNA 12.1776 kcal/mol@LB@@LB@Position - mRNA 189 -- 221@LB@Position - sRNA 13 -- 44@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 37 -- 43@LB@
62	0.00332	0.1645	b1305	pspB	-5.29	0.278747	189 -- 201	34 -- 46	psp operon transcription co-activator	_____________188___________202\n_____________\|_____________\|\n5'-AUU...UCGUC_____________UGAGC...GUG-3'\n______________UAAGGAGUACUUA\n______________:\|\|\|:\|\|:\|\|\|\|\|\n______________GUUCUUCGUGAAU\n3'-UUU...AAUUC_____________UUUUU...CAA-5'\n_____________\|_____________\|\n_____________47____________33\n	195 -- 201	34 -- 40	-14.7021 kcal/mol	3.41245 kcal/mol	5.99897 kcal/mol	188 202@LB@ \| \|@LB@5'-AUU...UCGUC UGAGC...GUG-3'@LB@ UAAGGAGUACUUA@LB@ :\|\|\|:\|\|:\|\|\|\|\|@LB@ GUUCUUCGUGAAU@LB@3'-UUU...AAUUC UUUUU...CAA-5'@LB@ \| \|@LB@ 47 33@LB@@LB@@LB@Energy -5.29 kcal/mol@LB@Hybridization Energy -14.7021 kcal/mol@LB@Unfolding Energy - mRNA 3.41245 kcal/mol@LB@Unfolding Energy - sRNA 5.99897 kcal/mol@LB@@LB@Position - mRNA 189 -- 201@LB@Position - sRNA 34 -- 46@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 34 -- 40@LB@
81	0.005437	0.2146	b1073	flgB	-5.23	0.286610	229 -- 247	36 -- 53	flagellar component of cell-proximal portion of basal-body rod	_____________228_________________248\n_____________\|___________________\|\n5'-UGA...CUUAC____UCAA___________CAAUC...CCG-3'\n______________GUUU____CAAGAGGCGCU\n______________\|:\|\|____\|\|\|\|\|:\|\|:\|\|\n______________CGAA____GUUCUUCGUGA\n3'-UUU...UUGAA____UUC____________AUUUU...CAA-5'\n_____________\|___________________\|\n_____________54__________________35\n	241 -- 247	36 -- 42	-18.0666 kcal/mol	6.73003 kcal/mol	6.10238 kcal/mol	228 248@LB@ \| \|@LB@5'-UGA...CUUAC UCAA CAAUC...CCG-3'@LB@ GUUU CAAGAGGCGCU@LB@ \|:\|\| \|\|\|\|\|:\|\|:\|\|@LB@ CGAA GUUCUUCGUGA@LB@3'-UUU...UUGAA UUC AUUUU...CAA-5'@LB@ \| \|@LB@ 54 35@LB@@LB@@LB@Energy -5.23 kcal/mol@LB@Hybridization Energy -18.0666 kcal/mol@LB@Unfolding Energy - mRNA 6.73003 kcal/mol@LB@Unfolding Energy - sRNA 6.10238 kcal/mol@LB@@LB@Position - mRNA 229 -- 247@LB@Position - sRNA 36 -- 53@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 36 -- 42@LB@
191	0.02253	0.38	b3186	rplU	-5.10	0.305418	95 -- 102	34 -- 41	50S ribosomal subunit protein L21	_____________94_______103\n_____________\|________\|\n5'-UUA...ACUGU________UCAAA...UUG-3'\n______________AGCACUUG\n______________\|\|\|\|\|\|\|:\n______________UCGUGAAU\n3'-UUU...GUUCU________UUUUU...CAA-5'\n_____________\|________\|\n_____________42_______33\n	96 -- 102	34 -- 40	-9.60207 kcal/mol	2.88333 kcal/mol	1.6155 kcal/mol	94 103@LB@ \| \|@LB@5'-UUA...ACUGU UCAAA...UUG-3'@LB@ AGCACUUG@LB@ \|\|\|\|\|\|\|:@LB@ UCGUGAAU@LB@3'-UUU...GUUCU UUUUU...CAA-5'@LB@ \| \|@LB@ 42 33@LB@@LB@@LB@Energy -5.10 kcal/mol@LB@Hybridization Energy -9.60207 kcal/mol@LB@Unfolding Energy - mRNA 2.88333 kcal/mol@LB@Unfolding Energy - sRNA 1.6155 kcal/mol@LB@@LB@Position - mRNA 95 -- 102@LB@Position - sRNA 34 -- 41@LB@Position Seed - mRNA 96 -- 102@LB@Position Seed - sRNA 34 -- 40@LB@
131	0.01234	0.3033	b4139	aspA	-5.03	0.315570	237 -- 252	26 -- 41	aspartate ammonia-lyase	_____________236______________253\n_____________\|________________\|\n5'-GAU...UGUUG_____CA_________CAGCU...ACU-3'\n______________GGUAC__GGGAAGUUC\n______________:\|:\|\|__:::\|\|:\|\|\|\n______________UCGUG__UUUUUUAAG\n3'-UUU...GUUCU_____AA_________CAAUG...CAA-5'\n_____________\|________________\|\n_____________42_______________25\n	246 -- 252	26 -- 32	-10.8102 kcal/mol	4.127 kcal/mol	1.64829 kcal/mol	236 253@LB@ \| \|@LB@5'-GAU...UGUUG CA CAGCU...ACU-3'@LB@ GGUAC GGGAAGUUC@LB@ :\|:\|\| :::\|\|:\|\|\|@LB@ UCGUG UUUUUUAAG@LB@3'-UUU...GUUCU AA CAAUG...CAA-5'@LB@ \| \|@LB@ 42 25@LB@@LB@@LB@Energy -5.03 kcal/mol@LB@Hybridization Energy -10.8102 kcal/mol@LB@Unfolding Energy - mRNA 4.127 kcal/mol@LB@Unfolding Energy - sRNA 1.64829 kcal/mol@LB@@LB@Position - mRNA 237 -- 252@LB@Position - sRNA 26 -- 41@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 26 -- 32@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@
157	0.01701	0.3489	b3856	mobB	-4.94	0.329991	189 -- 197	52 -- 60	molybdopterin-guanine dinucleotide biosynthesis protein B	_____________188_______198\n_____________\|_________\|\n5'-GUG...CCAGA_________CCGAU...CCA-3'\n______________GGAGCUUGC\n______________\|:\|:\|\|\|\|\|\n______________CUUUGAACG\n3'-UUU...CCCUA_________AAUUC...CAA-5'\n_____________\|_________\|\n_____________61________51\n	191 -- 197	52 -- 58	-10.6989 kcal/mol	2.59286 kcal/mol	3.16562 kcal/mol	188 198@LB@ \| \|@LB@5'-GUG...CCAGA CCGAU...CCA-3'@LB@ GGAGCUUGC@LB@ \|:\|:\|\|\|\|\|@LB@ CUUUGAACG@LB@3'-UUU...CCCUA AAUUC...CAA-5'@LB@ \| \|@LB@ 61 51@LB@@LB@@LB@Energy -4.94 kcal/mol@LB@Hybridization Energy -10.6989 kcal/mol@LB@Unfolding Energy - mRNA 2.59286 kcal/mol@LB@Unfolding Energy - sRNA 3.16562 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 52 -- 60@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 52 -- 58@LB@
161	0.01751	0.3504	b3394	hofN	-4.92	0.333288	275 -- 286	18 -- 29	DNA catabolic putative fimbrial assembly protein	_____________274__________287\n_____________\|____________\|\n5'-UGG...CUGAU____________UCUGC...CCG-3'\n______________GUUCGUUGCGCC\n______________:\|\|\|\|\|\|:\|:\|\|\n______________UAAGCAAUGUGG\n3'-UUU...UUUUU____________UCCUU...CAA-5'\n_____________\|____________\|\n_____________30___________17\n	275 -- 281	23 -- 29	-17.9024 kcal/mol	4.53191 kcal/mol	8.4513 kcal/mol	274 287@LB@ \| \|@LB@5'-UGG...CUGAU UCUGC...CCG-3'@LB@ GUUCGUUGCGCC@LB@ :\|\|\|\|\|\|:\|:\|\|@LB@ UAAGCAAUGUGG@LB@3'-UUU...UUUUU UCCUU...CAA-5'@LB@ \| \|@LB@ 30 17@LB@@LB@@LB@Energy -4.92 kcal/mol@LB@Hybridization Energy -17.9024 kcal/mol@LB@Unfolding Energy - mRNA 4.53191 kcal/mol@LB@Unfolding Energy - sRNA 8.4513 kcal/mol@LB@@LB@Position - mRNA 275 -- 286@LB@Position - sRNA 18 -- 29@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 23 -- 29@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@

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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