Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
80	0.01119	0.4523	b0241	phoE	-11.22	0.054424	189 -- 234	2 -- 43	outer membrane phosphoporin protein E	_____________188____________________________________________235\n_____________\|______________________________________________\|\n5'-AGC...UAAAA__________AA____AAAAGAGCACUCU__CA_____________GCAUU...AUG-3'\n______________UCAGGAAUGA__AUGA_____________GG__UUAGUGGUGAUGG\n______________\|\|\|\|:\|\|\|\|\|__\|\|\|\|_____________:\|__\|\|\|:\|\|:\|\|\|\|:\|\n______________AGUCUUUACU__UACU_____________UC__AAUUACUACUAUC\n3'-UUU...CUGUA________________GCCAUUAUUUAUU_________________G-5'\n_____________\|______________________________________________\|\n_____________44_____________________________________________1\n	228 -- 234	2 -- 8	-27.55 kcal/mol	10.0434 kcal/mol	6.29139 kcal/mol	188 235@LB@ \| \|@LB@5'-AGC...UAAAA AA AAAAGAGCACUCU CA GCAUU...AUG-3'@LB@ UCAGGAAUGA AUGA GG UUAGUGGUGAUGG@LB@ \|\|\|\|:\|\|\|\|\| \|\|\|\| :\| \|\|\|:\|\|:\|\|\|\|:\|@LB@ AGUCUUUACU UACU UC AAUUACUACUAUC@LB@3'-UUU...CUGUA GCCAUUAUUUAUU G-5'@LB@ \| \|@LB@ 44 1@LB@@LB@@LB@Energy -11.22 kcal/mol@LB@Hybridization Energy -27.55 kcal/mol@LB@Unfolding Energy - mRNA 10.0434 kcal/mol@LB@Unfolding Energy - sRNA 6.29139 kcal/mol@LB@@LB@Position - mRNA 189 -- 234@LB@Position - sRNA 2 -- 43@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 2 -- 8@LB@
89	0.01433	0.5059	b0636	rlmH	-12.18	0.033475	189 -- 207	1 -- 19	23S rRNA m(3)Psi1915 pseudouridine methyltransferase SAM-dependent	_____________188__________________208\n_____________\|____________________\|\n5'-CGG...AACUC___________C________UGCAA...UCG-3'\n______________UGGAGUUAAUG_GUGA_AGC\n______________\|::\|\|\|\|\|\|\|\|_:\|\|\|_\|\|\|\n______________AUUUCAAUUAC_UACU_UCG\n3'-UUU...UAUUU________________A___-5'\n_____________\|___________________\|\n_____________20__________________1\n	193 -- 199	9 -- 15	-16.4949 kcal/mol	4.25175 kcal/mol	0.0638423 kcal/mol	188 208@LB@ \| \|@LB@5'-CGG...AACUC C UGCAA...UCG-3'@LB@ UGGAGUUAAUG GUGA AGC@LB@ \|::\|\|\|\|\|\|\|\| :\|\|\| \|\|\|@LB@ AUUUCAAUUAC UACU UCG@LB@3'-UUU...UAUUU A -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -12.18 kcal/mol@LB@Hybridization Energy -16.4949 kcal/mol@LB@Unfolding Energy - mRNA 4.25175 kcal/mol@LB@Unfolding Energy - sRNA 0.0638423 kcal/mol@LB@@LB@Position - mRNA 189 -- 207@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 9 -- 15@LB@
14	0.0005823	0.1358	b4348	hsdS	-17.02	0.002033	190 -- 210	27 -- 58	specificity determinant for hsdM and hsdR	_____________189______________________________211\n_____________\|________________________________\|\n5'-CUG...UUGGU________________________________GGAAA...UAA-3'\n______________GGGGUGA__________AGGAAUGAGUG_CGG\n______________\|\|\|\|\|:\|__________\|\|:\|\|\|\|\|:\|\|_\|\|\|\n______________CCCCAUU__________UCUUUACUUAC_GCC\n3'-UUU...UUUAU_______UGUCUGUAAG___________U___AUUAU...UCG-5'\n_____________\|________________________________\|\n_____________59_______________________________26\n	190 -- 196	52 -- 58	-27.0928 kcal/mol	3.78881 kcal/mol	6.28755 kcal/mol	189 211@LB@ \| \|@LB@5'-CUG...UUGGU GGAAA...UAA-3'@LB@ GGGGUGA AGGAAUGAGUG CGG@LB@ \|\|\|\|\|:\| \|\|:\|\|\|\|\|:\|\| \|\|\|@LB@ CCCCAUU UCUUUACUUAC GCC@LB@3'-UUU...UUUAU UGUCUGUAAG U AUUAU...UCG-5'@LB@ \| \|@LB@ 59 26@LB@@LB@@LB@Energy -17.02 kcal/mol@LB@Hybridization Energy -27.0928 kcal/mol@LB@Unfolding Energy - mRNA 3.78881 kcal/mol@LB@Unfolding Energy - sRNA 6.28755 kcal/mol@LB@@LB@Position - mRNA 190 -- 210@LB@Position - sRNA 27 -- 58@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 52 -- 58@LB@
78	0.01113	0.4523	b2678	proW	-13.08	0.020853	190 -- 200	49 -- 59	glycine betaine/proline ABC transporter permease	_____________189_________201\n_____________\|___________\|\n5'-GUU...CGUGA___________AUGGC...ACG-3'\n______________GGGGGUAAAUA\n______________:\|\|\|\|\|\|\|\|:\|\n______________UCCCCAUUUGU\n3'-UUU...CUUUA___________CUGUA...UCG-5'\n_____________\|___________\|\n_____________60__________48\n	194 -- 200	49 -- 55	-15.0309 kcal/mol	1.22377 kcal/mol	0.730523 kcal/mol	189 201@LB@ \| \|@LB@5'-GUU...CGUGA AUGGC...ACG-3'@LB@ GGGGGUAAAUA@LB@ :\|\|\|\|\|\|\|\|:\|@LB@ UCCCCAUUUGU@LB@3'-UUU...CUUUA CUGUA...UCG-5'@LB@ \| \|@LB@ 60 48@LB@@LB@@LB@Energy -13.08 kcal/mol@LB@Hybridization Energy -15.0309 kcal/mol@LB@Unfolding Energy - mRNA 1.22377 kcal/mol@LB@Unfolding Energy - sRNA 0.730523 kcal/mol@LB@@LB@Position - mRNA 190 -- 200@LB@Position - sRNA 49 -- 59@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 49 -- 55@LB@
118	0.01863	0.5155	b0738	tolR	-11.80	0.040697	190 -- 199	50 -- 59	membrane spanning protein in TolA-TolQ-TolR complex	_____________189________200\n_____________\|__________\|\n5'-UGG...CAACA__________CAUGG...UGG-3'\n______________AGGGGUAAGC\n______________\|\|\|\|\|\|\|\|:\|\n______________UCCCCAUUUG\n3'-UUU...CUUUA__________UCUGU...UCG-5'\n_____________\|__________\|\n_____________60_________49\n	193 -- 199	50 -- 56	-16.6396 kcal/mol	4.1136 kcal/mol	0.728772 kcal/mol	189 200@LB@ \| \|@LB@5'-UGG...CAACA CAUGG...UGG-3'@LB@ AGGGGUAAGC@LB@ \|\|\|\|\|\|\|\|:\|@LB@ UCCCCAUUUG@LB@3'-UUU...CUUUA UCUGU...UCG-5'@LB@ \| \|@LB@ 60 49@LB@@LB@@LB@Energy -11.80 kcal/mol@LB@Hybridization Energy -16.6396 kcal/mol@LB@Unfolding Energy - mRNA 4.1136 kcal/mol@LB@Unfolding Energy - sRNA 0.728772 kcal/mol@LB@@LB@Position - mRNA 190 -- 199@LB@Position - sRNA 50 -- 59@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 50 -- 56@LB@
126	0.01995	0.5155	b2452	eutH	-9.16	0.141344	190 -- 206	5 -- 22	ethanolamine transporter	_____________189________________207\n_____________\|__________________\|\n5'-UUG...ACAGG________GC________AUUAA...UCC-3'\n______________GAGUAAAG__GAUGG_GA\n______________:\|:\|\|\|\|\|__:\|\|\|:_\|\|\n______________UUUAUUUC__UUACU_CU\n3'-UUU...CAUUA________AA_____A__AUCG-5'\n_____________\|__________________\|\n_____________23_________________4\n	191 -- 197	15 -- 21	-11.7395 kcal/mol	2.48279 kcal/mol	0.0977783 kcal/mol	189 207@LB@ \| \|@LB@5'-UUG...ACAGG GC AUUAA...UCC-3'@LB@ GAGUAAAG GAUGG GA@LB@ :\|:\|\|\|\|\| :\|\|\|: \|\|@LB@ UUUAUUUC UUACU CU@LB@3'-UUU...CAUUA AA A AUCG-5'@LB@ \| \|@LB@ 23 4@LB@@LB@@LB@Energy -9.16 kcal/mol@LB@Hybridization Energy -11.7395 kcal/mol@LB@Unfolding Energy - mRNA 2.48279 kcal/mol@LB@Unfolding Energy - sRNA 0.0977783 kcal/mol@LB@@LB@Position - mRNA 190 -- 206@LB@Position - sRNA 5 -- 22@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 15 -- 21@LB@
154	0.02518	0.526	b1602	pntB	-9.01	0.150855	190 -- 197	52 -- 59	pyridine nucleotide transhydrogenase beta subunit	_____________189______198\n_____________\|________\|\n5'-GCU...AAUUA________CAUAU...GUA-3'\n______________AGGGGUAA\n______________\|\|\|\|\|\|\|\|\n______________UCCCCAUU\n3'-UUU...CUUUA________UGUCU...UCG-5'\n_____________\|________\|\n_____________60_______51\n	191 -- 197	52 -- 58	-12.5664 kcal/mol	3.49825 kcal/mol	0.0599826 kcal/mol	189 198@LB@ \| \|@LB@5'-GCU...AAUUA CAUAU...GUA-3'@LB@ AGGGGUAA@LB@ \|\|\|\|\|\|\|\|@LB@ UCCCCAUU@LB@3'-UUU...CUUUA UGUCU...UCG-5'@LB@ \| \|@LB@ 60 51@LB@@LB@@LB@Energy -9.01 kcal/mol@LB@Hybridization Energy -12.5664 kcal/mol@LB@Unfolding Energy - mRNA 3.49825 kcal/mol@LB@Unfolding Energy - sRNA 0.0599826 kcal/mol@LB@@LB@Position - mRNA 190 -- 197@LB@Position - sRNA 52 -- 59@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 52 -- 58@LB@
17	0.000872	0.1482	b3940	metL	-12.03	0.036099	191 -- 199	51 -- 59	Bifunctional aspartokinase/homoserine dehydrogenase 2	_____________190_______200\n_____________\|_________\|\n5'-ACG...AAACA_________AAUGA...GCA-3'\n______________AGGGGUAAA\n______________\|\|\|\|\|\|\|\|\|\n______________UCCCCAUUU\n3'-UUU...CUUUA_________GUCUG...UCG-5'\n_____________\|_________\|\n_____________60________50\n	193 -- 199	51 -- 57	-13.5839 kcal/mol	1.01846 kcal/mol	0.532875 kcal/mol	190 200@LB@ \| \|@LB@5'-ACG...AAACA AAUGA...GCA-3'@LB@ AGGGGUAAA@LB@ \|\|\|\|\|\|\|\|\|@LB@ UCCCCAUUU@LB@3'-UUU...CUUUA GUCUG...UCG-5'@LB@ \| \|@LB@ 60 50@LB@@LB@@LB@Energy -12.03 kcal/mol@LB@Hybridization Energy -13.5839 kcal/mol@LB@Unfolding Energy - mRNA 1.01846 kcal/mol@LB@Unfolding Energy - sRNA 0.532875 kcal/mol@LB@@LB@Position - mRNA 191 -- 199@LB@Position - sRNA 51 -- 59@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 51 -- 57@LB@
103	0.01627	0.5059	b3527	yhjJ	-12.72	0.025178	191 -- 250	1 -- 59	putative periplasmic M16 family chaperone	_____________190_____________________________________________________________________251\n_____________\|_______________________________________________________________________\|\n5'-CUC...UGAUC______UC___U___GGGCACAAAAA____ACUUUUAGCG____________________C__________CACUG...GGC-3'\n______________AGGGGU__ACA_GCA___________UUCG__________GGCGGU___________UUG_UGAUGAUGGC\n______________\|\|\|\|\|\|__\|\|\|_:\|\|___________\|\|\|:__________\|:\|\|\|\|___________\|\|:_\|\|\|\|\|\|\|:\|\|\n______________UCCCCA__UGU_UGU___________AAGU__________CUGCCA___________AAU_ACUACUAUCG\n3'-UUU...CUUUA______UU___C__________________CUUUACUUA_______UUAUUUAUUUC___U__________-5'\n_____________\|______________________________________________________________________\|\n_____________60_____________________________________________________________________1\n	244 -- 250	1 -- 7	-34.0873 kcal/mol	15.0257 kcal/mol	6.33764 kcal/mol	190 251@LB@ \| \|@LB@5'-CUC...UGAUC UC U GGGCACAAAAA ACUUUUAGCG C CACUG...GGC-3'@LB@ AGGGGU ACA GCA UUCG GGCGGU UUG UGAUGAUGGC@LB@ \|\|\|\|\|\| \|\|\| :\|\| \|\|\|: \|:\|\|\|\| \|\|: \|\|\|\|\|\|\|:\|\|@LB@ UCCCCA UGU UGU AAGU CUGCCA AAU ACUACUAUCG@LB@3'-UUU...CUUUA UU C CUUUACUUA UUAUUUAUUUC U -5'@LB@ \| \|@LB@ 60 1@LB@@LB@@LB@Energy -12.72 kcal/mol@LB@Hybridization Energy -34.0873 kcal/mol@LB@Unfolding Energy - mRNA 15.0257 kcal/mol@LB@Unfolding Energy - sRNA 6.33764 kcal/mol@LB@@LB@Position - mRNA 191 -- 250@LB@Position - sRNA 1 -- 59@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 1 -- 7@LB@
113	0.01802	0.5155	b3910	yiiM	-13.90	0.013248	191 -- 239	40 -- 92	6-N-hydroxylaminopurine resistance protein	_____________190______________________________________________________240\n_____________\|________________________________________________________\|\n5'-UAA...GUGGA________A_____________________U_________C_______AGA_____GCUUA...UGC-3'\n______________GAGGGAAC__GAUGCGA__UAUCCGGUUGA_GUA____UA_ACAGGCA___UUCAG\n______________:\|:::\|\|\|__:\|\|\|\|\|\|__:\|\|\|\|\|\|\|\|\|\|_:\|\|____\|\|_\|\|\|\|:\|\|___\|\|\|\|\|\n______________UUUUUUUG__UUACGCU__GUAGGCCAACU_UAU____AU_UGUCUGU___AAGUC\n__________3'-U________GC_______CC___________U___CCCC__U_______________UUUAC...UCG-5'\n_____________\|________________________________________________________\|\n_____________93_______________________________________________________39\n	225 -- 231	45 -- 51	-43.4237 kcal/mol	10.1845 kcal/mol	19.3361 kcal/mol	190 240@LB@ \| \|@LB@5'-UAA...GUGGA A U C AGA GCUUA...UGC-3'@LB@ GAGGGAAC GAUGCGA UAUCCGGUUGA GUA UA ACAGGCA UUCAG@LB@ :\|:::\|\|\| :\|\|\|\|\|\| :\|\|\|\|\|\|\|\|\|\| :\|\| \|\| \|\|\|\|:\|\| \|\|\|\|\|@LB@ UUUUUUUG UUACGCU GUAGGCCAACU UAU AU UGUCUGU AAGUC@LB@ 3'-U GC CC U CCCC U UUUAC...UCG-5'@LB@ \| \|@LB@ 93 39@LB@@LB@@LB@Energy -13.90 kcal/mol@LB@Hybridization Energy -43.4237 kcal/mol@LB@Unfolding Energy - mRNA 10.1845 kcal/mol@LB@Unfolding Energy - sRNA 19.3361 kcal/mol@LB@@LB@Position - mRNA 191 -- 239@LB@Position - sRNA 40 -- 92@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 45 -- 51@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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