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	Additional homologs
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@
62	0.01306	0.6177	b4034	malE	-9.62	0.049140	112 -- 120	45 -- 53	maltose transporter subunit		_____________111_______121\n_____________\|_________\|\n5'-AGG...AGGGG_________UGGAA...UGG-3'\n______________CAAGGAGGA\n______________\|\|\|:\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	114 -- 120	45 -- 51	-12.5673 kcal/mol	2.02865 kcal/mol	0.917553 kcal/mol	111 121@LB@ \| \|@LB@5'-AGG...AGGGG UGGAA...UGG-3'@LB@ CAAGGAGGA@LB@ \|\|\|:\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -9.62 kcal/mol@LB@Hybridization Energy -12.5673 kcal/mol@LB@Unfolding Energy - mRNA 2.02865 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 112 -- 120@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 114 -- 120@LB@Position Seed - sRNA 45 -- 51@LB@
43	0.008509	0.6129	b4322	uxuA	-11.91	0.016653	184 -- 195	44 -- 55	mannonate hydrolase		_____________183__________196\n_____________\|____________\|\n5'-CAU...ACUAU__G_________AAAUC...AUA-3'\n______________GU_AAAGAGGAA\n______________\|\|_\|\|\|\|\|\|\|\|\|\n______________CA_UUUCUCCUU\n3'-UUU...CCGGG__G_________AAAGU...ACA-5'\n_____________\|____________\|\n_____________56___________43\n	189 -- 195	44 -- 50	-15.5118 kcal/mol	2.65561 kcal/mol	0.941432 kcal/mol	183 196@LB@ \| \|@LB@5'-CAU...ACUAU G AAAUC...AUA-3'@LB@ GU AAAGAGGAA@LB@ \|\| \|\|\|\|\|\|\|\|\|@LB@ CA UUUCUCCUU@LB@3'-UUU...CCGGG G AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -11.91 kcal/mol@LB@Hybridization Energy -15.5118 kcal/mol@LB@Unfolding Energy - mRNA 2.65561 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 184 -- 195@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 44 -- 50@LB@
89	0.01853	0.6177	b1448	mnaT	-8.57	0.080000	123 -- 134	43 -- 54	methionine N-acyltransferase; L-amino acid N-acyltransferase		_____________122__________135\n_____________\|____________\|\n5'-CGC...UAAUU___UC_______CCGUU...CGG-3'\n______________UCA__GAGGAAU\n______________\|\|\|__\|\|\|\|\|\|\|\n______________AGU__CUCCUUA\n3'-UUU...CGGGC___UU_______AAGUA...ACA-5'\n_____________\|____________\|\n_____________55___________42\n	128 -- 134	43 -- 49	-11.9422 kcal/mol	2.42412 kcal/mol	0.944705 kcal/mol	122 135@LB@ \| \|@LB@5'-CGC...UAAUU UC CCGUU...CGG-3'@LB@ UCA GAGGAAU@LB@ \|\|\| \|\|\|\|\|\|\|@LB@ AGU CUCCUUA@LB@3'-UUU...CGGGC UU AAGUA...ACA-5'@LB@ \| \|@LB@ 55 42@LB@@LB@@LB@Energy -8.57 kcal/mol@LB@Hybridization Energy -11.9422 kcal/mol@LB@Unfolding Energy - mRNA 2.42412 kcal/mol@LB@Unfolding Energy - sRNA 0.944705 kcal/mol@LB@@LB@Position - mRNA 123 -- 134@LB@Position - sRNA 43 -- 54@LB@Position Seed - mRNA 128 -- 134@LB@Position Seed - sRNA 43 -- 49@LB@
84	0.01785	0.6177	b4318	fimF	-9.06	0.063721	96 -- 107	44 -- 55	minor component of type 1 fimbriae	b1504 b0943	_____________95___________108\n_____________\|____________\|\n5'-CAU...AAUGG_GA_________AAUGC...UCA-3'\n______________G__GAAGAGGAA\n______________\|__:\|\|\|\|\|\|\|\|\n______________C__UUUCUCCUU\n3'-UUU...CCGGG_AG_________AAAGU...ACA-5'\n_____________\|____________\|\n_____________56___________43\n	101 -- 107	44 -- 50	-12.9705 kcal/mol	2.96464 kcal/mol	0.941432 kcal/mol	95 108@LB@ \| \|@LB@5'-CAU...AAUGG GA AAUGC...UCA-3'@LB@ G GAAGAGGAA@LB@ \| :\|\|\|\|\|\|\|\|@LB@ C UUUCUCCUU@LB@3'-UUU...CCGGG AG AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -9.06 kcal/mol@LB@Hybridization Energy -12.9705 kcal/mol@LB@Unfolding Energy - mRNA 2.96464 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 96 -- 107@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 44 -- 50@LB@
7	0.001184	0.5444	b0817	mntR	-11.99	0.016054	285 -- 294	46 -- 55	Mn(2+)-responsive manganese regulon transcriptional regulator		_____________284________295\n_____________\|__________\|\n5'-CUU...GCCAG__________CGCAUC-3'\n______________GUCAGAGAGG\n______________\|\|\|\|:\|\|\|\|\|\n______________CAGUUUCUCC\n3'-UUU...CCGGG__________UUAAA...ACA-5'\n_____________\|__________\|\n_____________56_________45\n	288 -- 294	46 -- 52	-16.1275 kcal/mol	3.21103 kcal/mol	0.924411 kcal/mol	284 295@LB@ \| \|@LB@5'-CUU...GCCAG CGCAUC-3'@LB@ GUCAGAGAGG@LB@ \|\|\|\|:\|\|\|\|\|@LB@ CAGUUUCUCC@LB@3'-UUU...CCGGG UUAAA...ACA-5'@LB@ \| \|@LB@ 56 45@LB@@LB@@LB@Energy -11.99 kcal/mol@LB@Hybridization Energy -16.1275 kcal/mol@LB@Unfolding Energy - mRNA 3.21103 kcal/mol@LB@Unfolding Energy - sRNA 0.924411 kcal/mol@LB@@LB@Position - mRNA 285 -- 294@LB@Position - sRNA 46 -- 55@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 46 -- 52@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@
28	0.005242	0.6024	b0785	moaE	-11.01	0.025514	211 -- 232	52 -- 74	molybdopterin synthase large subunit		_____________210_____________________233\n_____________\|_______________________\|\n5'-AGA...AGAAA____A__________________GCCGU...CCU-3'\n______________CCAA_AUUGUUGUUGGUCCG_CA\n______________\|\|\|\|_\|\|:\|:\|:\|\|\|\|:\|\|\|_\|\|\n______________GGUU_UAGCGAUAACCGGGC_GU\n3'-UUU...UUACC____A_______________A__UUCUC...ACA-5'\n_____________\|_______________________\|\n_____________75______________________51\n	216 -- 222	63 -- 69	-28.4518 kcal/mol	6.10798 kcal/mol	11.3304 kcal/mol	210 233@LB@ \| \|@LB@5'-AGA...AGAAA A GCCGU...CCU-3'@LB@ CCAA AUUGUUGUUGGUCCG CA@LB@ \|\|\|\| \|\|:\|:\|:\|\|\|\|:\|\|\| \|\|@LB@ GGUU UAGCGAUAACCGGGC GU@LB@3'-UUU...UUACC A A UUCUC...ACA-5'@LB@ \| \|@LB@ 75 51@LB@@LB@@LB@Energy -11.01 kcal/mol@LB@Hybridization Energy -28.4518 kcal/mol@LB@Unfolding Energy - mRNA 6.10798 kcal/mol@LB@Unfolding Energy - sRNA 11.3304 kcal/mol@LB@@LB@Position - mRNA 211 -- 232@LB@Position - sRNA 52 -- 74@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 63 -- 69@LB@
21	0.004054	0.5992	b2076	mdtC	-11.67	0.018717	158 -- 193	45 -- 78	multidrug efflux system subunit C		_____________157____________________________________194\n_____________\|______________________________________\|\n5'-CUC...GCAUU____A____AAGC____UU__________UG_______GGCGU...CGG-3'\n______________GUGG_CCAA____CGCU____GCCCGUCA__AAGAGGA\n______________:\|\|\|_\|\|\|\|____\|\|\|\|____\|\|\|\|\|\|\|\|__\|\|\|\|\|\|\|\n______________UACC_GGUU____GCGA____CGGGCAGU__UUCUCCU\n_____3'-UUUUUU_________AUA_____UAAC_________________UAAAG...ACA-5'\n_____________\|______________________________________\|\n_____________79_____________________________________44\n	187 -- 193	45 -- 51	-37.8051 kcal/mol	12.6053 kcal/mol	13.5316 kcal/mol	157 194@LB@ \| \|@LB@5'-CUC...GCAUU A AAGC UU UG GGCGU...CGG-3'@LB@ GUGG CCAA CGCU GCCCGUCA AAGAGGA@LB@ :\|\|\| \|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UACC GGUU GCGA CGGGCAGU UUCUCCU@LB@ 3'-UUUUUU AUA UAAC UAAAG...ACA-5'@LB@ \| \|@LB@ 79 44@LB@@LB@@LB@Energy -11.67 kcal/mol@LB@Hybridization Energy -37.8051 kcal/mol@LB@Unfolding Energy - mRNA 12.6053 kcal/mol@LB@Unfolding Energy - sRNA 13.5316 kcal/mol@LB@@LB@Position - mRNA 158 -- 193@LB@Position - sRNA 45 -- 78@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 45 -- 51@LB@
51	0.009714	0.6129	b1736	chbA	-9.09	0.063099	186 -- 194	44 -- 52	N N'-diacetylchitobiose-specific enzyme IIA component of PTS		_____________185_______195\n_____________\|_________\|\n5'-GGU...AGAAA_________CGAUG...GCC-3'\n______________AGAGAGGAA\n______________\|:\|\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	188 -- 194	44 -- 50	-11.469 kcal/mol	1.52278 kcal/mol	0.860683 kcal/mol	185 195@LB@ \| \|@LB@5'-GGU...AGAAA CGAUG...GCC-3'@LB@ AGAGAGGAA@LB@ \|:\|\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -9.09 kcal/mol@LB@Hybridization Energy -11.469 kcal/mol@LB@Unfolding Energy - mRNA 1.52278 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 186 -- 194@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@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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