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
8	0.001474	0.5928	b1048	opgG	-11.67	0.018726	159 -- 168	44 -- 53	OPG biosynthetic periplasmic beta-1 6 branching glycosyltransferase	_____________158________169\n_____________\|__________\|\n5'-ACA...GCACA__________AGUGC...AAU-3'\n______________CAAAGGGGGA\n______________\|\|\|\|\|:\|\|:\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	162 -- 168	44 -- 50	-12.9473 kcal/mol	0.352192 kcal/mol	0.927997 kcal/mol	158 169@LB@ \| \|@LB@5'-ACA...GCACA AGUGC...AAU-3'@LB@ CAAAGGGGGA@LB@ \|\|\|\|\|:\|\|:\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -11.67 kcal/mol@LB@Hybridization Energy -12.9473 kcal/mol@LB@Unfolding Energy - mRNA 0.352192 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 159 -- 168@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 44 -- 50@LB@
120	0.02398	0.6177	b0283	paoD	-10.02	0.040757	188 -- 198	44 -- 54	moco insertion factor for PaoABC aldehyde oxidoreductase	_____________187_________199\n_____________\|___________\|\n5'-AGG...GUGGU___________CAAUG...AGG-3'\n______________UUAAGGAGGAA\n______________\|:\|\|:\|\|\|\|\|\|\n______________AGUUUCUCCUU\n3'-UUU...CGGGC___________AAAGU...ACA-5'\n_____________\|___________\|\n_____________55__________43\n	192 -- 198	44 -- 50	-12.5456 kcal/mol	1.58604 kcal/mol	0.939671 kcal/mol	187 199@LB@ \| \|@LB@5'-AGG...GUGGU CAAUG...AGG-3'@LB@ UUAAGGAGGAA@LB@ \|:\|\|:\|\|\|\|\|\|@LB@ AGUUUCUCCUU@LB@3'-UUU...CGGGC AAAGU...ACA-5'@LB@ \| \|@LB@ 55 43@LB@@LB@@LB@Energy -10.02 kcal/mol@LB@Hybridization Energy -12.5456 kcal/mol@LB@Unfolding Energy - mRNA 1.58604 kcal/mol@LB@Unfolding Energy - sRNA 0.939671 kcal/mol@LB@@LB@Position - mRNA 188 -- 198@LB@Position - sRNA 44 -- 54@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 44 -- 50@LB@
134	0.02619	0.6177	b1126	potA	-9.47	0.052791	285 -- 299	37 -- 55	spermidine/putrescine ABC transporter ATPase	_____________284_________________300\n_____________\|___________________\|\n5'-CAA...UUGAU_GU________________C-3'\n______________G__AAAGAGG____UCAUU\n______________\|__\|\|\|\|\|\|\|____\|\|\|\|\|\n______________C__UUUCUCC____AGUAA\n3'-UUU...CCGGG_AG_______UUAA_____AAAAA...ACA-5'\n_____________\|___________________\|\n_____________56__________________36\n	288 -- 294	46 -- 52	-11.4861 kcal/mol	0.840334 kcal/mol	1.17789 kcal/mol	284 300@LB@ \| \|@LB@5'-CAA...UUGAU GU C-3'@LB@ G AAAGAGG UCAUU@LB@ \| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ C UUUCUCC AGUAA@LB@3'-UUU...CCGGG AG UUAA AAAAA...ACA-5'@LB@ \| \|@LB@ 56 36@LB@@LB@@LB@Energy -9.47 kcal/mol@LB@Hybridization Energy -11.4861 kcal/mol@LB@Unfolding Energy - mRNA 0.840334 kcal/mol@LB@Unfolding Energy - sRNA 1.17789 kcal/mol@LB@@LB@Position - mRNA 285 -- 299@LB@Position - sRNA 37 -- 55@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 46 -- 52@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@
108	0.0217	0.6177	b0243	proA	-8.76	0.073409	183 -- 193	47 -- 57	gamma-glutamylphosphate reductase	_____________182_________194\n_____________\|___________\|\n5'-AAU...AUUAC___________CAGGC...AUG-3'\n______________CCGUUAAGGAG\n______________\|\|\|\|:\|\|:\|\|\|\n______________GGCAGUUUCUC\n3'-UUU...AACCG___________CUUAA...ACA-5'\n_____________\|___________\|\n_____________58__________46\n	187 -- 193	47 -- 53	-14.7866 kcal/mol	3.29159 kcal/mol	2.73556 kcal/mol	182 194@LB@ \| \|@LB@5'-AAU...AUUAC CAGGC...AUG-3'@LB@ CCGUUAAGGAG@LB@ \|\|\|\|:\|\|:\|\|\|@LB@ GGCAGUUUCUC@LB@3'-UUU...AACCG CUUAA...ACA-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -8.76 kcal/mol@LB@Hybridization Energy -14.7866 kcal/mol@LB@Unfolding Energy - mRNA 3.29159 kcal/mol@LB@Unfolding Energy - sRNA 2.73556 kcal/mol@LB@@LB@Position - mRNA 183 -- 193@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 47 -- 53@LB@
106	0.02162	0.6177	b1831	proQ	-7.28	0.143813	159 -- 202	38 -- 75	RNA chaperone putative ProP translation regulator	_____________158_____________________________________________203\n_____________\|_______________________________________________\|\n5'-UUA...UUCAU___UG______U________A____CGUUGU__UC___A________GGAAA...CGC-3'\n______________GCC_____CGC_UGUUGGCU_CGUC______AA__AGG_AAUUUCAU\n______________\|\|\|_____\|\|\|_\|:\|\|\|\|\|:_\|\|\|\|______\|\|__\|\|\|_\|\|\|\|\|\|\|\|\n______________CGG_____GCG_AUAACCGG_GCAG______UU__UCC_UUAAAGUA\n3'-UUU...UUUAC___UUAUA_________________________UC____________AAAAA...ACA-5'\n_____________\|_______________________________________________\|\n_____________76______________________________________________37\n	196 -- 202	38 -- 44	-31.8607 kcal/mol	10.974 kcal/mol	13.6034 kcal/mol	158 203@LB@ \| \|@LB@5'-UUA...UUCAU UG U A CGUUGU UC A GGAAA...CGC-3'@LB@ GCC CGC UGUUGGCU CGUC AA AGG AAUUUCAU@LB@ \|\|\| \|\|\| \|:\|\|\|\|\|: \|\|\|\| \|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ CGG GCG AUAACCGG GCAG UU UCC UUAAAGUA@LB@3'-UUU...UUUAC UUAUA UC AAAAA...ACA-5'@LB@ \| \|@LB@ 76 37@LB@@LB@@LB@Energy -7.28 kcal/mol@LB@Hybridization Energy -31.8607 kcal/mol@LB@Unfolding Energy - mRNA 10.974 kcal/mol@LB@Unfolding Energy - sRNA 13.6034 kcal/mol@LB@@LB@Position - mRNA 159 -- 202@LB@Position - sRNA 38 -- 75@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 38 -- 44@LB@
179	0.03684	0.6177	b0335	prpE	-7.81	0.113441	203 -- 221	38 -- 55	propionate--CoA ligase	_____________202_________________222\n_____________\|___________________\|\n5'-GCC...AUUAU___UUUU__C_________CAGCG...AAA-3'\n______________GUC____AG_GAAUUUUAU\n______________\|\|\|____\|\|_\|\|\|\|\|\|:\|\|\n______________CAG____UC_CUUAAAGUA\n3'-UUU...CCGGG___UUUC____________AAAAA...ACA-5'\n_____________\|___________________\|\n_____________56__________________37\n	215 -- 221	38 -- 44	-10.8576 kcal/mol	1.87676 kcal/mol	1.17036 kcal/mol	202 222@LB@ \| \|@LB@5'-GCC...AUUAU UUUU C CAGCG...AAA-3'@LB@ GUC AG GAAUUUUAU@LB@ \|\|\| \|\| \|\|\|\|\|\|:\|\|@LB@ CAG UC CUUAAAGUA@LB@3'-UUU...CCGGG UUUC AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -7.81 kcal/mol@LB@Hybridization Energy -10.8576 kcal/mol@LB@Unfolding Energy - mRNA 1.87676 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 203 -- 221@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 38 -- 44@LB@
32	0.006131	0.6129	b2585	pssA	-9.74	0.046374	32 -- 41	45 -- 54	phosphatidylserine synthase; CDP-diacylglycerol-serine O-phosphatidyltransferase	_____________31_________42\n_____________\|__________\|\n5'-CGC...CCAGC__________GAUCG...CCG-3'\n______________UCGAAGAGGG\n______________\|\|:\|\|\|\|\|\|:\n______________AGUUUCUCCU\n3'-UUU...CGGGC__________UAAAG...ACA-5'\n_____________\|__________\|\n_____________55_________44\n	35 -- 41	45 -- 51	-13.2862 kcal/mol	2.61225 kcal/mol	0.929144 kcal/mol	31 42@LB@ \| \|@LB@5'-CGC...CCAGC GAUCG...CCG-3'@LB@ UCGAAGAGGG@LB@ \|\|:\|\|\|\|\|\|:@LB@ AGUUUCUCCU@LB@3'-UUU...CGGGC UAAAG...ACA-5'@LB@ \| \|@LB@ 55 44@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -13.2862 kcal/mol@LB@Unfolding Energy - mRNA 2.61225 kcal/mol@LB@Unfolding Energy - sRNA 0.929144 kcal/mol@LB@@LB@Position - mRNA 32 -- 41@LB@Position - sRNA 45 -- 54@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 45 -- 51@LB@
92	0.01873	0.6177	b2297	pta	-7.94	0.106741	187 -- 219	22 -- 52	phosphate acetyltransferase	_____________186_______________________________220\n_____________\|_________________________________\|\n5'-CGC...UAACG________UAAAC___GUCCCG___________UGAUC...GUC-3'\n______________AAAGAGGA_____CGU______UAUUAUUAUGC\n______________\|\|\|\|\|\|\|\|_____\|:\|______\|\|\|\|\|\|\|\|\|\|\|\n______________UUUCUCCU_____GUA______AUAAUAAUACG\n3'-UUU...GGCAG________UAAA____AAAAA____________GCAGU...ACA-5'\n_____________\|_________________________________\|\n_____________53________________________________21\n	213 -- 219	22 -- 28	-21.7034 kcal/mol	9.76868 kcal/mol	3.9903 kcal/mol	186 220@LB@ \| \|@LB@5'-CGC...UAACG UAAAC GUCCCG UGAUC...GUC-3'@LB@ AAAGAGGA CGU UAUUAUUAUGC@LB@ \|\|\|\|\|\|\|\| \|:\| \|\|\|\|\|\|\|\|\|\|\|@LB@ UUUCUCCU GUA AUAAUAAUACG@LB@3'-UUU...GGCAG UAAA AAAAA GCAGU...ACA-5'@LB@ \| \|@LB@ 53 21@LB@@LB@@LB@Energy -7.94 kcal/mol@LB@Hybridization Energy -21.7034 kcal/mol@LB@Unfolding Energy - mRNA 9.76868 kcal/mol@LB@Unfolding Energy - sRNA 3.9903 kcal/mol@LB@@LB@Position - mRNA 187 -- 219@LB@Position - sRNA 22 -- 52@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 22 -- 28@LB@
76	0.01599	0.6177	b1849	purT	-9.18	0.060248	187 -- 212	25 -- 50	phosphoribosylglycinamide formyltransferase 2	_____________186________________________213\n_____________\|__________________________\|\n5'-UUU...UAAUC______UA______AUGAC_______GGCAC...GUC-3'\n______________AGGGGA__UUCGUU_____GUUAUUA\n______________\|\|:\|\|\|__\|\|\|:\|\|_____:\|\|\|\|\|\|\n______________UCUCCU__AAGUAA_____UAAUAAU\n3'-UUU...CAGUU______UA______AAAAA_______ACGGC...ACA-5'\n_____________\|__________________________\|\n_____________51_________________________24\n	206 -- 212	25 -- 31	-15.1619 kcal/mol	4.88468 kcal/mol	1.09239 kcal/mol	186 213@LB@ \| \|@LB@5'-UUU...UAAUC UA AUGAC GGCAC...GUC-3'@LB@ AGGGGA UUCGUU GUUAUUA@LB@ \|\|:\|\|\| \|\|\|:\|\| :\|\|\|\|\|\|@LB@ UCUCCU AAGUAA UAAUAAU@LB@3'-UUU...CAGUU UA AAAAA ACGGC...ACA-5'@LB@ \| \|@LB@ 51 24@LB@@LB@@LB@Energy -9.18 kcal/mol@LB@Hybridization Energy -15.1619 kcal/mol@LB@Unfolding Energy - mRNA 4.88468 kcal/mol@LB@Unfolding Energy - sRNA 1.09239 kcal/mol@LB@@LB@Position - mRNA 187 -- 212@LB@Position - sRNA 25 -- 50@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 25 -- 31@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)

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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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