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
75	0.01076	0.4523	b4291	fecA	-8.60	0.179326	183 -- 193	2 -- 12	TonB-dependent outer membrane ferric citrate transporter and signal transducer; ferric citrate extracelluar receptor; FecR-interacting protein	_____________182_________194\n_____________\|___________\|\n5'-AGC...ACAAA___________GGAAG...CUG-3'\n______________AAUGAUGAUGG\n______________\|\|\|\|\|\|\|\|\|:\|\n______________UUACUACUAUC\n3'-UUU...UUCAA___________G-5'\n_____________\|___________\|\n_____________13__________1\n	187 -- 193	2 -- 8	-12.8036 kcal/mol	4.16536 kcal/mol	0.0386655 kcal/mol	182 194@LB@ \| \|@LB@5'-AGC...ACAAA GGAAG...CUG-3'@LB@ AAUGAUGAUGG@LB@ \|\|\|\|\|\|\|\|\|:\|@LB@ UUACUACUAUC@LB@3'-UUU...UUCAA G-5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -12.8036 kcal/mol@LB@Unfolding Energy - mRNA 4.16536 kcal/mol@LB@Unfolding Energy - sRNA 0.0386655 kcal/mol@LB@@LB@Position - mRNA 183 -- 193@LB@Position - sRNA 2 -- 12@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 2 -- 8@LB@
57	0.007764	0.4472	b0585	fes	-12.40	0.029926	182 -- 237	1 -- 55	enterobactin/ferrienterobactin esterase	_____________181___________________________________________________________238\n_____________\|_____________________________________________________________\|\n5'-CAU...GCACA_______U__G____________U_______CGU____AGU__GA_____GAGC_______AGUCG...GGU-3'\n______________GUAAACA_GG_GUU_____AUGG_GUGACGG___UAAA___AG__AGUGA____UGGUGGC\n______________\|\|\|\|\|\|\|_\|:_:\|\|_____\|\|\|:_:\|\|\|\|\|\|___\|\|\|\|___\|\|__\|:\|\|\|____\|\|:\|:\|\|\n______________CAUUUGU_CU_UAA_____UACU_UACUGCC___AUUU___UC__UUACU____ACUAUCG\n3'-UUU...AUCCC__________G___GUCUU____________AUU____AUU__AA________________-5'\n_____________\|____________________________________________________________\|\n_____________56___________________________________________________________1\n	231 -- 237	1 -- 7	-34.1879 kcal/mol	15.4551 kcal/mol	6.33758 kcal/mol	181 238@LB@ \| \|@LB@5'-CAU...GCACA U G U CGU AGU GA GAGC AGUCG...GGU-3'@LB@ GUAAACA GG GUU AUGG GUGACGG UAAA AG AGUGA UGGUGGC@LB@ \|\|\|\|\|\|\| \|: :\|\| \|\|\|: :\|\|\|\|\|\| \|\|\|\| \|\| \|:\|\|\| \|\|:\|:\|\|@LB@ CAUUUGU CU UAA UACU UACUGCC AUUU UC UUACU ACUAUCG@LB@3'-UUU...AUCCC G GUCUU AUU AUU AA -5'@LB@ \| \|@LB@ 56 1@LB@@LB@@LB@Energy -12.40 kcal/mol@LB@Hybridization Energy -34.1879 kcal/mol@LB@Unfolding Energy - mRNA 15.4551 kcal/mol@LB@Unfolding Energy - sRNA 6.33758 kcal/mol@LB@@LB@Position - mRNA 182 -- 237@LB@Position - sRNA 1 -- 55@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 1 -- 7@LB@
146	0.02455	0.526	b0491	fetB	-8.60	0.179526	114 -- 156	14 -- 57	iron export ABC transporter permease; peroxide resistance protein	_____________113_______________________________________________157\n_____________\|_________________________________________________\|\n5'-GCC...GCUGU______C___C____AAGAC_____U___CAU_________________GAUUA...AGA-3'\n______________GGGUGA_ACA_GAUA_____GAAAU_AAU___GCGG______AUAAAGU\n______________\|\|\|\|:\|_\|\|\|_\|\|:\|_____\|\|\|\|\|_\|\|\|___:\|\|\|______\|\|\|\|\|\|\|\n______________CCCAUU_UGU_CUGU_____CUUUA_UUA___UGCC______UAUUUCA\n3'-UUU...UUAUC_______________AAGU______C___C______AUUAUU_______AUUAC...UCG-5'\n_____________\|_________________________________________________\|\n_____________58________________________________________________13\n	150 -- 156	14 -- 20	-22.3302 kcal/mol	7.40722 kcal/mol	6.32606 kcal/mol	113 157@LB@ \| \|@LB@5'-GCC...GCUGU C C AAGAC U CAU GAUUA...AGA-3'@LB@ GGGUGA ACA GAUA GAAAU AAU GCGG AUAAAGU@LB@ \|\|\|\|:\| \|\|\| \|\|:\| \|\|\|\|\| \|\|\| :\|\|\| \|\|\|\|\|\|\|@LB@ CCCAUU UGU CUGU CUUUA UUA UGCC UAUUUCA@LB@3'-UUU...UUAUC AAGU C C AUUAUU AUUAC...UCG-5'@LB@ \| \|@LB@ 58 13@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -22.3302 kcal/mol@LB@Unfolding Energy - mRNA 7.40722 kcal/mol@LB@Unfolding Energy - sRNA 6.32606 kcal/mol@LB@@LB@Position - mRNA 114 -- 156@LB@Position - sRNA 14 -- 57@LB@Position Seed - mRNA 150 -- 156@LB@Position Seed - sRNA 14 -- 20@LB@
198	0.03373	0.5555	b3915	fieF	-7.92	0.235762	278 -- 297	1 -- 19	ferrous iron and zinc transporter	_____________277__________________298\n_____________\|____________________\|\n5'-AAA...CUGAU____A__UU__C________AUA-3'\n______________UAAA_UU__UG_AUGGUGGU\n______________\|\|\|\|_\|\|__\|\|_\|\|\|:\|:\|:\n______________AUUU_AA__AC_UACUAUCG\n3'-UUU...UAUUU____C__UU___________-5'\n_____________\|___________________\|\n_____________20__________________1\n	291 -- 297	1 -- 7	-10.0103 kcal/mol	2.02347 kcal/mol	0.0638423 kcal/mol	277 298@LB@ \| \|@LB@5'-AAA...CUGAU A UU C AUA-3'@LB@ UAAA UU UG AUGGUGGU@LB@ \|\|\|\| \|\| \|\| \|\|\|:\|:\|:@LB@ AUUU AA AC UACUAUCG@LB@3'-UUU...UAUUU C UU -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -7.92 kcal/mol@LB@Hybridization Energy -10.0103 kcal/mol@LB@Unfolding Energy - mRNA 2.02347 kcal/mol@LB@Unfolding Energy - sRNA 0.0638423 kcal/mol@LB@@LB@Position - mRNA 278 -- 297@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 1 -- 7@LB@
83	0.0117	0.4626	b1071	flgM	-8.58	0.180603	153 -- 179	1 -- 25	anti-sigma factor for FliA (sigma 28)	_____________152_________________________180\n_____________\|___________________________\|\n5'-CCA...UUGCC__________CAACAC_____AAA___GCCCU...CAA-3'\n______________GAUAAAUAAG______AUGAU___AGC\n______________:\|\|\|\|\|\|\|\|:______\|\|\|\|\|___\|\|\|\n______________UUAUUUAUUU______UACUA___UCG\n3'-UUU...UGCCA__________CAAU_______CUA___-5'\n_____________\|__________________________\|\n_____________26_________________________1\n	156 -- 162	16 -- 22	-10.1551 kcal/mol	1.46038 kcal/mol	0.112205 kcal/mol	152 180@LB@ \| \|@LB@5'-CCA...UUGCC CAACAC AAA GCCCU...CAA-3'@LB@ GAUAAAUAAG AUGAU AGC@LB@ :\|\|\|\|\|\|\|\|: \|\|\|\|\| \|\|\|@LB@ UUAUUUAUUU UACUA UCG@LB@3'-UUU...UGCCA CAAU CUA -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -8.58 kcal/mol@LB@Hybridization Energy -10.1551 kcal/mol@LB@Unfolding Energy - mRNA 1.46038 kcal/mol@LB@Unfolding Energy - sRNA 0.112205 kcal/mol@LB@@LB@Position - mRNA 153 -- 179@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 16 -- 22@LB@
73	0.01069	0.4523	b1949	fliQ	-11.32	0.051762	219 -- 228	2 -- 11	flagellar biosynthesis protein	_____________218________229\n_____________\|__________\|\n5'-UUC...CGGUC__________GGACU...UUA-3'\n______________AUGAUGAUGG\n______________\|\|\|\|\|\|\|\|:\|\n______________UACUACUAUC\n3'-UUU...UCAAU__________G-5'\n_____________\|__________\|\n_____________12_________1\n	222 -- 228	2 -- 8	-12.2017 kcal/mol	0.859554 kcal/mol	0.0252227 kcal/mol	218 229@LB@ \| \|@LB@5'-UUC...CGGUC GGACU...UUA-3'@LB@ AUGAUGAUGG@LB@ \|\|\|\|\|\|\|\|:\|@LB@ UACUACUAUC@LB@3'-UUU...UCAAU G-5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -11.32 kcal/mol@LB@Hybridization Energy -12.2017 kcal/mol@LB@Unfolding Energy - mRNA 0.859554 kcal/mol@LB@Unfolding Energy - sRNA 0.0252227 kcal/mol@LB@@LB@Position - mRNA 219 -- 228@LB@Position - sRNA 2 -- 11@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 2 -- 8@LB@
124	0.01977	0.5155	b1920	fliY	-11.21	0.054671	192 -- 201	49 -- 58	cystine transporter subunit	_____________191________202\n_____________\|__________\|\n5'-CCA...CAUUC__________UGAAA...UGC-3'\n______________GGGGUGAAUA\n______________\|\|\|\|\|:\|\|:\|\n______________CCCCAUUUGU\n3'-UUU...UUUAU__________CUGUA...UCG-5'\n_____________\|__________\|\n_____________59_________48\n	195 -- 201	49 -- 55	-14.4557 kcal/mol	2.52037 kcal/mol	0.729386 kcal/mol	191 202@LB@ \| \|@LB@5'-CCA...CAUUC UGAAA...UGC-3'@LB@ GGGGUGAAUA@LB@ \|\|\|\|\|:\|\|:\|@LB@ CCCCAUUUGU@LB@3'-UUU...UUUAU CUGUA...UCG-5'@LB@ \| \|@LB@ 59 48@LB@@LB@@LB@Energy -11.21 kcal/mol@LB@Hybridization Energy -14.4557 kcal/mol@LB@Unfolding Energy - mRNA 2.52037 kcal/mol@LB@Unfolding Energy - sRNA 0.729386 kcal/mol@LB@@LB@Position - mRNA 192 -- 201@LB@Position - sRNA 49 -- 58@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 49 -- 55@LB@
119	0.019	0.5155	b0904	focA	-10.20	0.088413	192 -- 208	1 -- 18	formate channel	_____________191________________209\n_____________\|__________________\|\n5'-GAG...AAGAG______________A___UGACA...AGA-3'\n______________AGAGUUAGUG_UGA_AGC\n______________\|:\|\|\|\|\|:\|\|_\|\|\|_\|\|\|\n______________UUUCAAUUAC_ACU_UCG\n3'-UUU...AUUUA__________U___A___-5'\n_____________\|_________________\|\n_____________19________________1\n	195 -- 201	9 -- 15	-16.1977 kcal/mol	5.93514 kcal/mol	0.0611543 kcal/mol	191 209@LB@ \| \|@LB@5'-GAG...AAGAG A UGACA...AGA-3'@LB@ AGAGUUAGUG UGA AGC@LB@ \|:\|\|\|\|\|:\|\| \|\|\| \|\|\|@LB@ UUUCAAUUAC ACU UCG@LB@3'-UUU...AUUUA U A -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -16.1977 kcal/mol@LB@Unfolding Energy - mRNA 5.93514 kcal/mol@LB@Unfolding Energy - sRNA 0.0611543 kcal/mol@LB@@LB@Position - mRNA 192 -- 208@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 9 -- 15@LB@
92	0.01497	0.5059	b1902	ftnB	-10.62	0.072498	12 -- 36	1 -- 25	ferritin B putative ferrous iron reservoir	_____________11________________________37\n_____________\|_________________________\|\n5'-UGA...GUAAA____U_____C________UUA___AUUUU...AAC-3'\n______________AAUA_AUAAA_UUGAUGAU___AGC\n______________\|\|\|\|_\|\|\|\|\|_\|\|:\|\|\|\|\|___\|\|\|\n______________UUAU_UAUUU_AAUUACUA___UCG\n3'-UUU...UGCCA____U_____C________CUA___-5'\n_____________\|________________________\|\n_____________26_______________________1\n	24 -- 30	7 -- 13	-13.6335 kcal/mol	2.89836 kcal/mol	0.112205 kcal/mol	11 37@LB@ \| \|@LB@5'-UGA...GUAAA U C UUA AUUUU...AAC-3'@LB@ AAUA AUAAA UUGAUGAU AGC@LB@ \|\|\|\| \|\|\|\|\| \|\|:\|\|\|\|\| \|\|\|@LB@ UUAU UAUUU AAUUACUA UCG@LB@3'-UUU...UGCCA U C CUA -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -10.62 kcal/mol@LB@Hybridization Energy -13.6335 kcal/mol@LB@Unfolding Energy - mRNA 2.89836 kcal/mol@LB@Unfolding Energy - sRNA 0.112205 kcal/mol@LB@@LB@Position - mRNA 12 -- 36@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 7 -- 13@LB@
61	0.008575	0.4523	b3464	ftsY	-13.38	0.017655	71 -- 119	2 -- 50	Signal Recognition Particle (SRP) receptor	_____________70__________________________________________________120\n_____________\|___________________________________________________\|\n5'-CCC...UCCGC______ACACAUACUUGCA_______AU______U________________ACUAU...CGG-3'\n______________CAGAUA_____________GGCGGUG__GUGAAU_AAGUUAA__GUGAUAG\n______________\|\|\|\|:\|_____________\|:\|\|\|\|:__:\|:\|\|\|_\|\|\|\|\|\|\|__:\|\|\|\|\|\|\n______________GUCUGU_____________CUGCCAU__UAUUUA_UUCAAUU__UACUAUC\n3'-UUU...CAUUU______AAGUCUUUACUUA_______________U_______AC_______G-5'\n_____________\|___________________________________________________\|\n_____________51__________________________________________________1\n	113 -- 119	2 -- 8	-30.4135 kcal/mol	10.695 kcal/mol	6.33478 kcal/mol	70 120@LB@ \| \|@LB@5'-CCC...UCCGC ACACAUACUUGCA AU U ACUAU...CGG-3'@LB@ CAGAUA GGCGGUG GUGAAU AAGUUAA GUGAUAG@LB@ \|\|\|\|:\| \|:\|\|\|\|: :\|:\|\|\| \|\|\|\|\|\|\| :\|\|\|\|\|\|@LB@ GUCUGU CUGCCAU UAUUUA UUCAAUU UACUAUC@LB@3'-UUU...CAUUU AAGUCUUUACUUA U AC G-5'@LB@ \| \|@LB@ 51 1@LB@@LB@@LB@Energy -13.38 kcal/mol@LB@Hybridization Energy -30.4135 kcal/mol@LB@Unfolding Energy - mRNA 10.695 kcal/mol@LB@Unfolding Energy - sRNA 6.33478 kcal/mol@LB@@LB@Position - mRNA 71 -- 119@LB@Position - sRNA 2 -- 50@LB@Position Seed - mRNA 113 -- 119@LB@Position Seed - sRNA 2 -- 8@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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