Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
48	0.00405	0.2857	b0409	secF	-13.37	0.031213	166 -- 172	5 -- 11	SecYEG protein translocase auxillary subunit	_____________165_____173\n_____________\|_______\|\n5'-CUU...GGCAA_______AAGAA...UGU-3'\n______________GCGCGUC\n______________\|\|\|\|\|\|\|\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	166 -- 172	5 -- 11	-14.9857 kcal/mol	0.509172 kcal/mol	1.11145 kcal/mol	165 173@LB@ \| \|@LB@5'-CUU...GGCAA AAGAA...UGU-3'@LB@ GCGCGUC@LB@ \|\|\|\|\|\|\|@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -13.37 kcal/mol@LB@Hybridization Energy -14.9857 kcal/mol@LB@Unfolding Energy - mRNA 0.509172 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 166 -- 172@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 5 -- 11@LB@
34	0.002145	0.2094	b1939	fliG	-13.29	0.032191	145 -- 162	6 -- 22	flagellar motor switching and energizing component	_____________144________________163\n_____________\|__________________\|\n5'-AGC...AUGUC_________UCC______GGUGG...AAG-3'\n______________UGAUAACGA___GCGCGU\n______________\|\|\|\|\|\|\|:\|___\|\|\|\|\|\|\n______________ACUAUUGUU___CGCGCA\n3'-UUU...CUACU_________UA_______GAAAG-5'\n_____________\|__________________\|\n_____________23_________________5\n	147 -- 153	14 -- 20	-19.5862 kcal/mol	5.04831 kcal/mol	1.24718 kcal/mol	144 163@LB@ \| \|@LB@5'-AGC...AUGUC UCC GGUGG...AAG-3'@LB@ UGAUAACGA GCGCGU@LB@ \|\|\|\|\|\|\|:\| \|\|\|\|\|\|@LB@ ACUAUUGUU CGCGCA@LB@3'-UUU...CUACU UA GAAAG-5'@LB@ \| \|@LB@ 23 5@LB@@LB@@LB@Energy -13.29 kcal/mol@LB@Hybridization Energy -19.5862 kcal/mol@LB@Unfolding Energy - mRNA 5.04831 kcal/mol@LB@Unfolding Energy - sRNA 1.24718 kcal/mol@LB@@LB@Position - mRNA 145 -- 162@LB@Position - sRNA 6 -- 22@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 14 -- 20@LB@
29	0.001844	0.2094	b2047	wcaJ	-13.26	0.032615	200 -- 222	7 -- 21	colanic biosynthesis UDP-glucose lipid carrier transferase	_____________199_____________________223\n_____________\|_______________________\|\n5'-GCA...ACAAC__________CUAAAAAA_____AGCGA...UAU-3'\n______________GAUGACAAAU________GCGCG\n______________\|\|\|:\|\|\|\|\|\|________\|\|\|\|\|\n______________CUAUUGUUUA________CGCGC\n3'-UUU...UACUA_______________________AGAAAG-5'\n_____________\|_______________________\|\n_____________22______________________6\n	203 -- 209	12 -- 18	-17.5174 kcal/mol	3.01646 kcal/mol	1.24179 kcal/mol	199 223@LB@ \| \|@LB@5'-GCA...ACAAC CUAAAAAA AGCGA...UAU-3'@LB@ GAUGACAAAU GCGCG@LB@ \|\|\|:\|\|\|\|\|\| \|\|\|\|\|@LB@ CUAUUGUUUA CGCGC@LB@3'-UUU...UACUA AGAAAG-5'@LB@ \| \|@LB@ 22 6@LB@@LB@@LB@Energy -13.26 kcal/mol@LB@Hybridization Energy -17.5174 kcal/mol@LB@Unfolding Energy - mRNA 3.01646 kcal/mol@LB@Unfolding Energy - sRNA 1.24179 kcal/mol@LB@@LB@Position - mRNA 200 -- 222@LB@Position - sRNA 7 -- 21@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 12 -- 18@LB@
199	0.01944	0.3104	b3657	yicJ	-13.22	0.033173	129 -- 161	8 -- 45	putative transporter	_____________128_____________________________________162\n_____________\|_______________________________________\|\n5'-CAG...GAAUA_________CA_____________UU____A________UAUCG...UGU-3'\n______________UUCG_CUCU_____CAGGGAUGGU____AC_AAAUGCGU\n______________\|\|\|:_\|\|\|\|_____\|\|\|\|\|\|\|\|:\|____\|\|_\|\|\|\|\|\|\|:\n______________AAGU_GAGA_____GUCCCUACUA____UG_UUUACGCG\n3'-UUU...UUUUA____A____CUUAA__________CUAU___________CAGAAAG-5'\n_____________\|_______________________________________\|\n_____________46______________________________________7\n	155 -- 161	8 -- 14	-30.3918 kcal/mol	7.7216 kcal/mol	9.45195 kcal/mol	128 162@LB@ \| \|@LB@5'-CAG...GAAUA CA UU A UAUCG...UGU-3'@LB@ UUCG CUCU CAGGGAUGGU AC AAAUGCGU@LB@ \|\|\|: \|\|\|\| \|\|\|\|\|\|\|\|:\| \|\| \|\|\|\|\|\|\|:@LB@ AAGU GAGA GUCCCUACUA UG UUUACGCG@LB@3'-UUU...UUUUA A CUUAA CUAU CAGAAAG-5'@LB@ \| \|@LB@ 46 7@LB@@LB@@LB@Energy -13.22 kcal/mol@LB@Hybridization Energy -30.3918 kcal/mol@LB@Unfolding Energy - mRNA 7.7216 kcal/mol@LB@Unfolding Energy - sRNA 9.45195 kcal/mol@LB@@LB@Position - mRNA 129 -- 161@LB@Position - sRNA 8 -- 45@LB@Position Seed - mRNA 155 -- 161@LB@Position Seed - sRNA 8 -- 14@LB@
36	0.002407	0.2206	b2550	yphH	-13.17	0.033778	238 -- 251	7 -- 20	putative DNA-binding transcriptional regulator	_____________237____________252\n_____________\|______________\|\n5'-AGG...CCACC______________AUUCU...UGG-3'\n______________AUAACAAAUGCGUG\n______________\|\|\|\|\|\|\|\|\|\|\|\|:\|\n______________UAUUGUUUACGCGC\n3'-UUU...ACUAC______________AGAAAG-5'\n_____________\|______________\|\n_____________21_____________6\n	245 -- 251	7 -- 13	-19.0929 kcal/mol	4.67933 kcal/mol	1.23906 kcal/mol	237 252@LB@ \| \|@LB@5'-AGG...CCACC AUUCU...UGG-3'@LB@ AUAACAAAUGCGUG@LB@ \|\|\|\|\|\|\|\|\|\|\|\|:\|@LB@ UAUUGUUUACGCGC@LB@3'-UUU...ACUAC AGAAAG-5'@LB@ \| \|@LB@ 21 6@LB@@LB@@LB@Energy -13.17 kcal/mol@LB@Hybridization Energy -19.0929 kcal/mol@LB@Unfolding Energy - mRNA 4.67933 kcal/mol@LB@Unfolding Energy - sRNA 1.23906 kcal/mol@LB@@LB@Position - mRNA 238 -- 251@LB@Position - sRNA 7 -- 20@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 7 -- 13@LB@
17	0.0005644	0.1124	b0949	uup	-13.14	0.034258	282 -- 297	4 -- 21	replication regulatory ABC-F family DNA-binding ATPase	_____________281________________298\n_____________\|__________________\|\n5'-GAU...UCGAA__________________GUC-3'\n______________GAUAACGAA__CGUGUUU\n______________\|\|\|\|\|\|:\|\|__\|\|:\|\|:\|\n______________CUAUUGUUU__GCGCAGA\n3'-UUU...UACUA_________AC_______AAG-5'\n_____________\|__________________\|\n_____________22_________________3\n	291 -- 297	4 -- 10	-16.3224 kcal/mol	1.92683 kcal/mol	1.2552 kcal/mol	281 298@LB@ \| \|@LB@5'-GAU...UCGAA GUC-3'@LB@ GAUAACGAA CGUGUUU@LB@ \|\|\|\|\|\|:\|\| \|\|:\|\|:\|@LB@ CUAUUGUUU GCGCAGA@LB@3'-UUU...UACUA AC AAG-5'@LB@ \| \|@LB@ 22 3@LB@@LB@@LB@Energy -13.14 kcal/mol@LB@Hybridization Energy -16.3224 kcal/mol@LB@Unfolding Energy - mRNA 1.92683 kcal/mol@LB@Unfolding Energy - sRNA 1.2552 kcal/mol@LB@@LB@Position - mRNA 282 -- 297@LB@Position - sRNA 4 -- 21@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 4 -- 10@LB@
56	0.005155	0.3024	b3091	uxaA	-13.05	0.035558	147 -- 159	6 -- 19	altronate hydrolase	_____________146____________160\n_____________\|______________\|\n5'-CUG...UGCUU______________GACUA...CGC-3'\n______________UAAC_AAUGCGCGU\n______________\|\|\|\|_\|\|\|\|\|\|\|\|\|\n______________AUUG_UUACGCGCA\n3'-UUU...CUACU____U_________GAAAG-5'\n_____________\|______________\|\n_____________20_____________5\n	153 -- 159	6 -- 12	-17.3524 kcal/mol	3.0727 kcal/mol	1.22941 kcal/mol	146 160@LB@ \| \|@LB@5'-CUG...UGCUU GACUA...CGC-3'@LB@ UAAC AAUGCGCGU@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ AUUG UUACGCGCA@LB@3'-UUU...CUACU U GAAAG-5'@LB@ \| \|@LB@ 20 5@LB@@LB@@LB@Energy -13.05 kcal/mol@LB@Hybridization Energy -17.3524 kcal/mol@LB@Unfolding Energy - mRNA 3.0727 kcal/mol@LB@Unfolding Energy - sRNA 1.22941 kcal/mol@LB@@LB@Position - mRNA 147 -- 159@LB@Position - sRNA 6 -- 19@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 6 -- 12@LB@
57	0.005155	0.3024	b3091	uxaA	-13.05	0.035558	147 -- 159	6 -- 19	altronate hydrolase	_____________146____________160\n_____________\|______________\|\n5'-CUG...UGCUU______________GACUA...CGC-3'\n______________UAAC_AAUGCGCGU\n______________\|\|\|\|_\|\|\|\|\|\|\|\|\|\n______________AUUG_UUACGCGCA\n3'-UUU...CUACU____U_________GAAAG-5'\n_____________\|______________\|\n_____________20_____________5\n	153 -- 159	6 -- 12	-17.3524 kcal/mol	3.0727 kcal/mol	1.22941 kcal/mol	146 160@LB@ \| \|@LB@5'-CUG...UGCUU GACUA...CGC-3'@LB@ UAAC AAUGCGCGU@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ AUUG UUACGCGCA@LB@3'-UUU...CUACU U GAAAG-5'@LB@ \| \|@LB@ 20 5@LB@@LB@@LB@Energy -13.05 kcal/mol@LB@Hybridization Energy -17.3524 kcal/mol@LB@Unfolding Energy - mRNA 3.0727 kcal/mol@LB@Unfolding Energy - sRNA 1.22941 kcal/mol@LB@@LB@Position - mRNA 147 -- 159@LB@Position - sRNA 6 -- 19@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 6 -- 12@LB@
16	0.0004819	0.102	b0957	ompA	-13.00	0.036257	182 -- 195	8 -- 22	outer membrane protein A (3a;II*;G;d)	_____________181_____________196\n_____________\|_______________\|\n5'-CUU...UUGGA_______________AAAAA...AAC-3'\n______________UGAUAACGAG_GCGC\n______________\|\|\|\|\|\|\|:\|:_\|\|\|\|\n______________ACUAUUGUUU_CGCG\n3'-UUU...CUACU__________A____CAGAAAG-5'\n_____________\|_______________\|\n_____________23______________7\n	185 -- 191	13 -- 19	-17.7455 kcal/mol	3.5039 kcal/mol	1.23838 kcal/mol	181 196@LB@ \| \|@LB@5'-CUU...UUGGA AAAAA...AAC-3'@LB@ UGAUAACGAG GCGC@LB@ \|\|\|\|\|\|\|:\|: \|\|\|\|@LB@ ACUAUUGUUU CGCG@LB@3'-UUU...CUACU A CAGAAAG-5'@LB@ \| \|@LB@ 23 7@LB@@LB@@LB@Energy -13.00 kcal/mol@LB@Hybridization Energy -17.7455 kcal/mol@LB@Unfolding Energy - mRNA 3.5039 kcal/mol@LB@Unfolding Energy - sRNA 1.23838 kcal/mol@LB@@LB@Position - mRNA 182 -- 195@LB@Position - sRNA 8 -- 22@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 13 -- 19@LB@
178	0.01756	0.3104	b2017	yefM	-12.99	0.036476	219 -- 231	5 -- 18	antitoxin of the YoeB-YefM toxin-antitoxin system	_____________218____________232\n_____________\|______________\|\n5'-AUU...GCUAC______________AGAAU...AUG-3'\n______________AGCGAA_GCGCGUC\n______________\|:\|:\|\|_\|\|\|\|\|\|\|\n______________UUGUUU_CGCGCAG\n3'-UUU...UACUA______A_______AAAG-5'\n_____________\|______________\|\n_____________19_____________4\n	225 -- 231	5 -- 11	-18.6086 kcal/mol	4.39571 kcal/mol	1.2243 kcal/mol	218 232@LB@ \| \|@LB@5'-AUU...GCUAC AGAAU...AUG-3'@LB@ AGCGAA GCGCGUC@LB@ \|:\|:\|\| \|\|\|\|\|\|\|@LB@ UUGUUU CGCGCAG@LB@3'-UUU...UACUA A AAAG-5'@LB@ \| \|@LB@ 19 4@LB@@LB@@LB@Energy -12.99 kcal/mol@LB@Hybridization Energy -18.6086 kcal/mol@LB@Unfolding Energy - mRNA 4.39571 kcal/mol@LB@Unfolding Energy - sRNA 1.2243 kcal/mol@LB@@LB@Position - mRNA 219 -- 231@LB@Position - sRNA 5 -- 18@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 5 -- 11@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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