Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
188	0.03926	0.6177	b4547	ypfN	-8.44	0.084930	187 -- 194	44 -- 51	putative membrane protein UPF0370 family	_____________186______195\n_____________\|________\|\n5'-UGA...UCUGC________AUAAG...AGA-3'\n______________AAGAGGAA\n______________\|\|\|\|\|\|\|\|\n______________UUCUCCUU\n3'-UUU...GCAGU________AAAGU...ACA-5'\n_____________\|________\|\n_____________52_______43\n	188 -- 194	44 -- 50	-10.245 kcal/mol	0.953219 kcal/mol	0.848077 kcal/mol	186 195@LB@ \| \|@LB@5'-UGA...UCUGC AUAAG...AGA-3'@LB@ AAGAGGAA@LB@ \|\|\|\|\|\|\|\|@LB@ UUCUCCUU@LB@3'-UUU...GCAGU AAAGU...ACA-5'@LB@ \| \|@LB@ 52 43@LB@@LB@@LB@Energy -8.44 kcal/mol@LB@Hybridization Energy -10.245 kcal/mol@LB@Unfolding Energy - mRNA 0.953219 kcal/mol@LB@Unfolding Energy - sRNA 0.848077 kcal/mol@LB@@LB@Position - mRNA 187 -- 194@LB@Position - sRNA 44 -- 51@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
46	0.009202	0.6129	b0183	rnhB	-8.44	0.085048	25 -- 32	48 -- 55	ribonuclease HII degrades RNA of DNA-RNA hybrids	_____________24_______33\n_____________\|________\|\n5'-AAU...AGUUA________AUUAU...UCC-3'\n______________GUCAAAGA\n______________\|\|\|\|\|\|\|\|\n______________CAGUUUCU\n3'-UUU...CCGGG________CCUUA...ACA-5'\n_____________\|________\|\n_____________56_______47\n	26 -- 32	48 -- 54	-9.30452 kcal/mol	0.544993 kcal/mol	0.318869 kcal/mol	24 33@LB@ \| \|@LB@5'-AAU...AGUUA AUUAU...UCC-3'@LB@ GUCAAAGA@LB@ \|\|\|\|\|\|\|\|@LB@ CAGUUUCU@LB@3'-UUU...CCGGG CCUUA...ACA-5'@LB@ \| \|@LB@ 56 47@LB@@LB@@LB@Energy -8.44 kcal/mol@LB@Hybridization Energy -9.30452 kcal/mol@LB@Unfolding Energy - mRNA 0.544993 kcal/mol@LB@Unfolding Energy - sRNA 0.318869 kcal/mol@LB@@LB@Position - mRNA 25 -- 32@LB@Position - sRNA 48 -- 55@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 48 -- 54@LB@
131	0.02569	0.6177	b0848	ybjM	-8.44	0.085177	187 -- 197	44 -- 55	inner membrane protein	_____________186__________198\n_____________\|____________\|\n5'-GAA...GCAGU____________CGAGU...GGG-3'\n______________GUC_AGGAGGAA\n______________\|\|\|_\|:\|\|\|\|\|\|\n______________CAG_UUCUCCUU\n3'-UUU...CCGGG___U________AAAGU...ACA-5'\n_____________\|____________\|\n_____________56___________43\n	191 -- 197	44 -- 50	-13.6185 kcal/mol	4.23971 kcal/mol	0.941432 kcal/mol	186 198@LB@ \| \|@LB@5'-GAA...GCAGU CGAGU...GGG-3'@LB@ GUC AGGAGGAA@LB@ \|\|\| \|:\|\|\|\|\|\|@LB@ CAG UUCUCCUU@LB@3'-UUU...CCGGG U AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -8.44 kcal/mol@LB@Hybridization Energy -13.6185 kcal/mol@LB@Unfolding Energy - mRNA 4.23971 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 187 -- 197@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 44 -- 50@LB@
148	0.02945	0.6177	b0692	potE	-8.42	0.085901	187 -- 195	44 -- 52	putrescine/proton symporter: putrescine/ornithine antiporter	_____________186_______196\n_____________\|_________\|\n5'-UGU...UGUUG_________AAAUU...AGC-3'\n______________AAAGGGGAA\n______________\|\|\|\|:\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	189 -- 195	44 -- 50	-10.6161 kcal/mol	1.33649 kcal/mol	0.860683 kcal/mol	186 196@LB@ \| \|@LB@5'-UGU...UGUUG AAAUU...AGC-3'@LB@ AAAGGGGAA@LB@ \|\|\|\|:\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.42 kcal/mol@LB@Hybridization Energy -10.6161 kcal/mol@LB@Unfolding Energy - mRNA 1.33649 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 187 -- 195@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 44 -- 50@LB@
119	0.02381	0.6177	b1434	ydcN	-8.41	0.086264	87 -- 94	43 -- 50	putative DNA-binding transcriptional regulator	_____________86_______95\n_____________\|________\|\n5'-CGG...UGGGU________AGAAA...CUA-3'\n______________GGAGGAAU\n______________:\|\|\|\|\|\|\|\n______________UCUCCUUA\n3'-UUU...CAGUU________AAGUA...ACA-5'\n_____________\|________\|\n_____________51_______42\n	88 -- 94	43 -- 49	-10.2233 kcal/mol	0.967994 kcal/mol	0.845564 kcal/mol	86 95@LB@ \| \|@LB@5'-CGG...UGGGU AGAAA...CUA-3'@LB@ GGAGGAAU@LB@ :\|\|\|\|\|\|\|@LB@ UCUCCUUA@LB@3'-UUU...CAGUU AAGUA...ACA-5'@LB@ \| \|@LB@ 51 42@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -10.2233 kcal/mol@LB@Unfolding Energy - mRNA 0.967994 kcal/mol@LB@Unfolding Energy - sRNA 0.845564 kcal/mol@LB@@LB@Position - mRNA 87 -- 94@LB@Position - sRNA 43 -- 50@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 43 -- 49@LB@
136	0.02642	0.6177	b4036	lamB	-8.19	0.095416	26 -- 54	55 -- 84	maltose outer membrane porin (maltoporin)	_____________25_____________________________55\n_____________\|______________________________\|\n5'-CGC...GGUAG_____________CAU_______C______CCGCC...GUU-3'\n______________AAGAAGGU_GCCA___UCGCUAU_GGCCUG\n______________\|\|:\|\|::\|_\|\|\|\|___\|\|\|\|\|\|\|_\|\|\|\|:\|\n______________UUUUUUUA_CGGU___AGCGAUA_CCGGGC\n___________3'-________C____UAU_______A______AGUUU...ACA-5'\n______________\|_____________________________\|\n______________84____________________________54\n	41 -- 47	62 -- 68	-32.2235 kcal/mol	10.7352 kcal/mol	13.2983 kcal/mol	25 55@LB@ \| \|@LB@5'-CGC...GGUAG CAU C CCGCC...GUU-3'@LB@ AAGAAGGU GCCA UCGCUAU GGCCUG@LB@ \|\|:\|\|::\| \|\|\|\| \|\|\|\|\|\|\| \|\|\|\|:\|@LB@ UUUUUUUA CGGU AGCGAUA CCGGGC@LB@ 3'- C UAU A AGUUU...ACA-5'@LB@ \| \|@LB@ 84 54@LB@@LB@@LB@Energy -8.19 kcal/mol@LB@Hybridization Energy -32.2235 kcal/mol@LB@Unfolding Energy - mRNA 10.7352 kcal/mol@LB@Unfolding Energy - sRNA 13.2983 kcal/mol@LB@@LB@Position - mRNA 26 -- 54@LB@Position - sRNA 55 -- 84@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 62 -- 68@LB@
70	0.01448	0.6177	b4012	yjaB	-8.12	0.098308	234 -- 242	44 -- 52	GNAT-family putative N-acetyltransferase; acetyl coenzyme A-binding protein	_____________233_______243\n_____________\|_________\|\n5'-AAG...AUGAG_________GAACU...CAG-3'\n______________GAAGGGGAG\n______________:\|\|\|:\|\|\|:\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	236 -- 242	44 -- 50	-9.78668 kcal/mol	0.80114 kcal/mol	0.860683 kcal/mol	233 243@LB@ \| \|@LB@5'-AAG...AUGAG GAACU...CAG-3'@LB@ GAAGGGGAG@LB@ :\|\|\|:\|\|\|:@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.12 kcal/mol@LB@Hybridization Energy -9.78668 kcal/mol@LB@Unfolding Energy - mRNA 0.80114 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 234 -- 242@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 44 -- 50@LB@
31	0.005902	0.6127	b1951	rcsA	-8.09	0.100100	163 -- 178	37 -- 51	transcriptional regulator of colanic acid capsular biosynthesis	_____________162______________179\n_____________\|________________\|\n5'-GUU...CAGGU__________A_____ACGCA...UUG-3'\n______________AAGGGGAAUU_UCGUU\n______________\|\|\|:\|\|\|\|\|\|_\|\|:\|\|\n______________UUCUCCUUAA_AGUAA\n3'-UUU...GCAGU________________AAAAA...ACA-5'\n_____________\|________________\|\n_____________52_______________36\n	166 -- 172	42 -- 48	-14.3412 kcal/mol	5.18535 kcal/mol	1.07049 kcal/mol	162 179@LB@ \| \|@LB@5'-GUU...CAGGU A ACGCA...UUG-3'@LB@ AAGGGGAAUU UCGUU@LB@ \|\|\|:\|\|\|\|\|\| \|\|:\|\|@LB@ UUCUCCUUAA AGUAA@LB@3'-UUU...GCAGU AAAAA...ACA-5'@LB@ \| \|@LB@ 52 36@LB@@LB@@LB@Energy -8.09 kcal/mol@LB@Hybridization Energy -14.3412 kcal/mol@LB@Unfolding Energy - mRNA 5.18535 kcal/mol@LB@Unfolding Energy - sRNA 1.07049 kcal/mol@LB@@LB@Position - mRNA 163 -- 178@LB@Position - sRNA 37 -- 51@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 42 -- 48@LB@
130	0.02541	0.6177	b4365	yjjQ	-8.08	0.100207	263 -- 277	38 -- 55	putative transcriptional regulator	_____________262_________________278\n_____________\|___________________\|\n5'-AGG...GCAGG___A_______________GAGGA...AUG-3'\n______________GUU_AAAGAGG____UCAU\n______________\|\|:_\|\|\|\|\|\|\|____\|\|\|\|\n______________CAG_UUUCUCC____AGUA\n3'-UUU...CCGGG___________UUAA____AAAAA...ACA-5'\n_____________\|___________________\|\n_____________56__________________37\n	267 -- 273	46 -- 52	-10.7142 kcal/mol	1.46087 kcal/mol	1.17036 kcal/mol	262 278@LB@ \| \|@LB@5'-AGG...GCAGG A GAGGA...AUG-3'@LB@ GUU AAAGAGG UCAU@LB@ \|\|: \|\|\|\|\|\|\| \|\|\|\|@LB@ CAG UUUCUCC AGUA@LB@3'-UUU...CCGGG UUAA AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -10.7142 kcal/mol@LB@Unfolding Energy - mRNA 1.46087 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 263 -- 277@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 46 -- 52@LB@
104	0.02144	0.6177	b2718	hycH	-8.07	0.100760	181 -- 190	46 -- 55	hydrogenase 3 maturation protein	_____________180________191\n_____________\|__________\|\n5'-CAG...AUGUU__________CGCGU...UGG-3'\n______________GUUGAAGAGG\n______________\|\|::\|\|\|\|\|\|\n______________CAGUUUCUCC\n3'-UUU...CCGGG__________UUAAA...ACA-5'\n_____________\|__________\|\n_____________56_________45\n	184 -- 190	46 -- 52	-11.8031 kcal/mol	2.8078 kcal/mol	0.924411 kcal/mol	180 191@LB@ \| \|@LB@5'-CAG...AUGUU CGCGU...UGG-3'@LB@ GUUGAAGAGG@LB@ \|\|::\|\|\|\|\|\|@LB@ CAGUUUCUCC@LB@3'-UUU...CCGGG UUAAA...ACA-5'@LB@ \| \|@LB@ 56 45@LB@@LB@@LB@Energy -8.07 kcal/mol@LB@Hybridization Energy -11.8031 kcal/mol@LB@Unfolding Energy - mRNA 2.8078 kcal/mol@LB@Unfolding Energy - sRNA 0.924411 kcal/mol@LB@@LB@Position - mRNA 181 -- 190@LB@Position - sRNA 46 -- 55@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 46 -- 52@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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