Input and runtime details for job 2727377 (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 2727377 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:09 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:28 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:18:35 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:18:43 CET 2018
	Job Completed		@ Fri Feb 16 20:19:11 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=2727377&toolName=CopraRNA ( 30 days expiry )

Description of the job

RyhB

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
101	0.01031	0.3393	b2314	dedD	-14.11	0.039362	188 -- 259	13 -- 86	membrane-anchored periplasmic protein involved in septation	_____________187______________________________________________________________________________260\n_____________\|________________________________________________________________________________\|\n5'-UUG...UUGAC__G__G_GAAG_______________GUUUCA___U____UA_______CGA______________GG_____U______GAUUG...AUU-3'\n______________GC_AG_A____CGG_UGGC_AAGUAA______GAA_CGGU__GUGGGCA___UCGUGCU____GGU____CGC_GGGGGU\n______________\|\|_\|\|_\|____\|\|\|_\|\|\|\|_\|\|\|\|\|\|______\|\|\|_\|::\|__\|\|\|:\|\|\|___\|\|\|\|\|\|\|____\|\|\|____\|\|\|_\|:\|\|\|\|\n______________CG_UC_U____GCC_ACCG_UUCAUU______CUU_GUUA__CACUCGU___AGCACGA____CCA____GCG_CUCCCA\n_______3'-UUUU__G__G_GG_____G____A______AUGAC____C_____________UAC_______AAGU___AGAG__________GAAGG...GCG-5'\n_____________\|________________________________________________________________________________\|\n_____________87_______________________________________________________________________________12\n	238 -- 244	33 -- 39	-62.0732 kcal/mol	22.3094 kcal/mol	25.6538 kcal/mol	187 260@LB@ \| \|@LB@5'-UUG...UUGAC G G GAAG GUUUCA U UA CGA GG U GAUUG...AUU-3'@LB@ GC AG A CGG UGGC AAGUAA GAA CGGU GUGGGCA UCGUGCU GGU CGC GGGGGU@LB@ \|\| \|\| \| \|\|\| \|\|\|\| \|\|\|\|\|\| \|\|\| \|::\| \|\|\|:\|\|\| \|\|\|\|\|\|\| \|\|\| \|\|\| \|:\|\|\|\|@LB@ CG UC U GCC ACCG UUCAUU CUU GUUA CACUCGU AGCACGA CCA GCG CUCCCA@LB@ 3'-UUUU G G GG G A AUGAC C UAC AAGU AGAG GAAGG...GCG-5'@LB@ \| \|@LB@ 87 12@LB@@LB@@LB@Energy -14.11 kcal/mol@LB@Hybridization Energy -62.0732 kcal/mol@LB@Unfolding Energy - mRNA 22.3094 kcal/mol@LB@Unfolding Energy - sRNA 25.6538 kcal/mol@LB@@LB@Position - mRNA 188 -- 259@LB@Position - sRNA 13 -- 86@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 33 -- 39@LB@
166	0.02064	0.4072	b0429	cyoD	-11.77	0.097498	188 -- 206	44 -- 59	cytochrome o ubiquinol oxidase subunit IV	_____________187_________________207\n_____________\|___________________\|\n5'-UUC...UCUGA____________AAU____CAUUC...UCU-3'\n______________UGGGGGCGAUGU___GAGU\n______________\|\|\|::\|\|:\|\|\|\|___\|\|\|:\n______________ACCUUCGUUACA___CUCG\n3'-UUU...UUAUG___________________UUACA...GCG-5'\n_____________\|___________________\|\n_____________60__________________43\n	193 -- 199	48 -- 54	-20.4312 kcal/mol	5.39053 kcal/mol	3.27056 kcal/mol	187 207@LB@ \| \|@LB@5'-UUC...UCUGA AAU CAUUC...UCU-3'@LB@ UGGGGGCGAUGU GAGU@LB@ \|\|\|::\|\|:\|\|\|\| \|\|\|:@LB@ ACCUUCGUUACA CUCG@LB@3'-UUU...UUAUG UUACA...GCG-5'@LB@ \| \|@LB@ 60 43@LB@@LB@@LB@Energy -11.77 kcal/mol@LB@Hybridization Energy -20.4312 kcal/mol@LB@Unfolding Energy - mRNA 5.39053 kcal/mol@LB@Unfolding Energy - sRNA 3.27056 kcal/mol@LB@@LB@Position - mRNA 188 -- 206@LB@Position - sRNA 44 -- 59@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 48 -- 54@LB@
58	0.00551	0.2905	b0156	erpA	-13.52	0.049632	189 -- 214	36 -- 60	iron-sulfur cluster insertion protein	_____________188_________________________215\n_____________\|___________________________\|\n5'-UAG...GUCGU__________AAUA_________A___AGCAC...UAC-3'\n______________UUGG_AGCAA____UGAGUGAUG_CGU\n______________:\|\|\|_\|\|\|\|\|____\|\|\|\|::\|\|\|_\|\|\|\n______________GACC_UCGUU____ACUCGUUAC_GCA\n3'-UUU...AUUAU____U_____AC___________A___CGAAA...GCG-5'\n_____________\|___________________________\|\n_____________61__________________________35\n	204 -- 210	40 -- 46	-21.0837 kcal/mol	4.26473 kcal/mol	3.30077 kcal/mol	188 215@LB@ \| \|@LB@5'-UAG...GUCGU AAUA A AGCAC...UAC-3'@LB@ UUGG AGCAA UGAGUGAUG CGU@LB@ :\|\|\| \|\|\|\|\| \|\|\|\|::\|\|\| \|\|\|@LB@ GACC UCGUU ACUCGUUAC GCA@LB@3'-UUU...AUUAU U AC A CGAAA...GCG-5'@LB@ \| \|@LB@ 61 35@LB@@LB@@LB@Energy -13.52 kcal/mol@LB@Hybridization Energy -21.0837 kcal/mol@LB@Unfolding Energy - mRNA 4.26473 kcal/mol@LB@Unfolding Energy - sRNA 3.30077 kcal/mol@LB@@LB@Position - mRNA 189 -- 214@LB@Position - sRNA 36 -- 60@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 40 -- 46@LB@
82	0.008223	0.3318	b1654	grxD	-11.69	0.100410	189 -- 207	43 -- 58	glutaredoxin-4	_____________188_________________208\n_____________\|___________________\|\n5'-AAA...UUUGA________GACAA______CCACU...CUG-3'\n______________GGAAGCAA_____UGAGCA\n______________\|\|\|\|\|\|\|\|_____\|\|\|\|\|\|\n______________CCUUCGUU_____ACUCGU\n3'-UUU...UAUGA________AC_________UACAG...GCG-5'\n_____________\|___________________\|\n_____________59__________________42\n	190 -- 196	51 -- 57	-19.1647 kcal/mol	4.26252 kcal/mol	3.20949 kcal/mol	188 208@LB@ \| \|@LB@5'-AAA...UUUGA GACAA CCACU...CUG-3'@LB@ GGAAGCAA UGAGCA@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ CCUUCGUU ACUCGU@LB@3'-UUU...UAUGA AC UACAG...GCG-5'@LB@ \| \|@LB@ 59 42@LB@@LB@@LB@Energy -11.69 kcal/mol@LB@Hybridization Energy -19.1647 kcal/mol@LB@Unfolding Energy - mRNA 4.26252 kcal/mol@LB@Unfolding Energy - sRNA 3.20949 kcal/mol@LB@@LB@Position - mRNA 189 -- 207@LB@Position - sRNA 43 -- 58@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 51 -- 57@LB@
89	0.009246	0.3393	b1279	yciS	-12.08	0.086714	189 -- 204	46 -- 61	DUF1049 family inner membrane protein function unknown	_____________188______________205\n_____________\|________________\|\n5'-ACC...ACAUA__G_____________AAUAU...UGU-3'\n______________AC_GGAAGUAAUGUGA\n______________\|\|_\|\|\|\|\|:\|\|\|\|\|\|\|\n______________UG_CCUUCGUUACACU\n3'-UUU...CAUUA__A_____________CGUUA...GCG-5'\n_____________\|________________\|\n_____________62_______________45\n	198 -- 204	46 -- 52	-21.4875 kcal/mol	6.16612 kcal/mol	3.24422 kcal/mol	188 205@LB@ \| \|@LB@5'-ACC...ACAUA G AAUAU...UGU-3'@LB@ AC GGAAGUAAUGUGA@LB@ \|\| \|\|\|\|\|:\|\|\|\|\|\|\|@LB@ UG CCUUCGUUACACU@LB@3'-UUU...CAUUA A CGUUA...GCG-5'@LB@ \| \|@LB@ 62 45@LB@@LB@@LB@Energy -12.08 kcal/mol@LB@Hybridization Energy -21.4875 kcal/mol@LB@Unfolding Energy - mRNA 6.16612 kcal/mol@LB@Unfolding Energy - sRNA 3.24422 kcal/mol@LB@@LB@Position - mRNA 189 -- 204@LB@Position - sRNA 46 -- 61@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 46 -- 52@LB@
13	0.000833	0.2153	b1531	marA	-8.74	0.292618	190 -- 205	38 -- 57	multiple antibiotic resistance transcriptional regulator	_____________189__________________206\n_____________\|____________________\|\n5'-AAG...AAAAA____________________CAGAC...AGC-3'\n______________GAGGUA___UGA_CGAUGUC\n______________\|\|:\|:\|___\|\|\|_\|:\|\|\|\|\|\n______________CUUCGU___ACU_GUUACAG\n3'-UUU...AUGAC______UAC___C_______CACGA...GCG-5'\n_____________\|____________________\|\n_____________58___________________37\n	199 -- 205	38 -- 44	-15.3925 kcal/mol	3.44101 kcal/mol	3.2161 kcal/mol	189 206@LB@ \| \|@LB@5'-AAG...AAAAA CAGAC...AGC-3'@LB@ GAGGUA UGA CGAUGUC@LB@ \|\|:\|:\| \|\|\| \|:\|\|\|\|\|@LB@ CUUCGU ACU GUUACAG@LB@3'-UUU...AUGAC UAC C CACGA...GCG-5'@LB@ \| \|@LB@ 58 37@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -15.3925 kcal/mol@LB@Unfolding Energy - mRNA 3.44101 kcal/mol@LB@Unfolding Energy - sRNA 3.2161 kcal/mol@LB@@LB@Position - mRNA 190 -- 205@LB@Position - sRNA 38 -- 57@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 38 -- 44@LB@
39	0.003417	0.2776	b4469	ygiQ	-15.58	0.022035	190 -- 206	44 -- 60	Radical SAM superfamily protein	_____________189_______________207\n_____________\|_________________\|\n5'-GCG...CAUUU__________AA_____UCUAU...CUC-3'\n______________CUGGAAGCAA__UGAGC\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\|\|\|\n______________GACCUUCGUU__ACUCG\n3'-UUU...AUUAU__________AC_____UUACA...GCG-5'\n_____________\|_________________\|\n_____________61________________43\n	193 -- 199	51 -- 57	-24.5566 kcal/mol	5.6787 kcal/mol	3.2985 kcal/mol	189 207@LB@ \| \|@LB@5'-GCG...CAUUU AA UCUAU...CUC-3'@LB@ CUGGAAGCAA UGAGC@LB@ \|\|\|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ GACCUUCGUU ACUCG@LB@3'-UUU...AUUAU AC UUACA...GCG-5'@LB@ \| \|@LB@ 61 43@LB@@LB@@LB@Energy -15.58 kcal/mol@LB@Hybridization Energy -24.5566 kcal/mol@LB@Unfolding Energy - mRNA 5.6787 kcal/mol@LB@Unfolding Energy - sRNA 3.2985 kcal/mol@LB@@LB@Position - mRNA 190 -- 206@LB@Position - sRNA 44 -- 60@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 51 -- 57@LB@
148	0.01761	0.3998	b4262	lptG	-10.98	0.131149	190 -- 206	42 -- 57	lipopolysaccharide export ABC permease	_____________189_______________207\n_____________\|_________________\|\n5'-CCA...GUAAA____________U____CCUUU...UCA-3'\n______________GGAGCGGUGUGA_GCAA\n______________\|:\|\|\|::\|\|\|\|\|_\|\|\|\|\n______________CUUCGUUACACU_CGUU\n3'-UUU...AUGAC_________________ACAGC...GCG-5'\n_____________\|_________________\|\n_____________58________________41\n	195 -- 201	46 -- 52	-21.8951 kcal/mol	7.70229 kcal/mol	3.20882 kcal/mol	189 207@LB@ \| \|@LB@5'-CCA...GUAAA U CCUUU...UCA-3'@LB@ GGAGCGGUGUGA GCAA@LB@ \|:\|\|\|::\|\|\|\|\| \|\|\|\|@LB@ CUUCGUUACACU CGUU@LB@3'-UUU...AUGAC ACAGC...GCG-5'@LB@ \| \|@LB@ 58 41@LB@@LB@@LB@Energy -10.98 kcal/mol@LB@Hybridization Energy -21.8951 kcal/mol@LB@Unfolding Energy - mRNA 7.70229 kcal/mol@LB@Unfolding Energy - sRNA 3.20882 kcal/mol@LB@@LB@Position - mRNA 190 -- 206@LB@Position - sRNA 42 -- 57@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 46 -- 52@LB@
176	0.02184	0.4113	b0153	fhuB	-8.75	0.291577	190 -- 208	42 -- 58	iron(3+)-hydroxamate import ABC transporter permease	_____________189_________________209\n_____________\|___________________\|\n5'-UAU...CCAUC________AGC________ACGAA...CGC-3'\n______________GGAGGUAA___GUGAGUAA\n______________\|\|\|:\|:\|\|___\|\|\|\|\|:\|\|\n______________CCUUCGUU___CACUCGUU\n3'-UUU...UAUGA________A__________ACAGC...GCG-5'\n_____________\|___________________\|\n_____________59__________________41\n	202 -- 208	42 -- 48	-20.4106 kcal/mol	8.45448 kcal/mol	3.2101 kcal/mol	189 209@LB@ \| \|@LB@5'-UAU...CCAUC AGC ACGAA...CGC-3'@LB@ GGAGGUAA GUGAGUAA@LB@ \|\|\|:\|:\|\| \|\|\|\|\|:\|\|@LB@ CCUUCGUU CACUCGUU@LB@3'-UUU...UAUGA A ACAGC...GCG-5'@LB@ \| \|@LB@ 59 41@LB@@LB@@LB@Energy -8.75 kcal/mol@LB@Hybridization Energy -20.4106 kcal/mol@LB@Unfolding Energy - mRNA 8.45448 kcal/mol@LB@Unfolding Energy - sRNA 3.2101 kcal/mol@LB@@LB@Position - mRNA 190 -- 208@LB@Position - sRNA 42 -- 58@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 42 -- 48@LB@
195	0.0249	0.4226	b1476	fdnI	-9.91	0.194140	190 -- 212	37 -- 58	formate dehydrogenase-N cytochrome B556 (gamma) subunit nitrate-inducible	_____________189______________________213\n_____________\|________________________\|\n5'-CGU...GACGA_____AU__UCA____________AAAAU...UUU-3'\n______________GGAGG__CA___UGAGUAA_GUCG\n______________\|\|\|:\|__\|\|___\|\|\|\|:\|\|_\|\|\|\|\n______________CCUUC__GU___ACUCGUU_CAGC\n3'-UUU...UAUGA_________UAC_______A____ACGAA...GCG-5'\n_____________\|________________________\|\n_____________59_______________________36\n	202 -- 208	42 -- 48	-19.5397 kcal/mol	6.39857 kcal/mol	3.22699 kcal/mol	189 213@LB@ \| \|@LB@5'-CGU...GACGA AU UCA AAAAU...UUU-3'@LB@ GGAGG CA UGAGUAA GUCG@LB@ \|\|\|:\| \|\| \|\|\|\|:\|\| \|\|\|\|@LB@ CCUUC GU ACUCGUU CAGC@LB@3'-UUU...UAUGA UAC A ACGAA...GCG-5'@LB@ \| \|@LB@ 59 36@LB@@LB@@LB@Energy -9.91 kcal/mol@LB@Hybridization Energy -19.5397 kcal/mol@LB@Unfolding Energy - mRNA 6.39857 kcal/mol@LB@Unfolding Energy - sRNA 3.22699 kcal/mol@LB@@LB@Position - mRNA 190 -- 212@LB@Position - sRNA 37 -- 58@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 42 -- 48@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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