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
72	0.01058	0.4523	b3458	livK	-8.91	0.157650	183 -- 215	28 -- 63	leucine transporter subunit	_____________182___________________________________216\n_____________\|_____________________________________\|\n5'-UGU...AUCAC________AUUUUU____UAU______CG________AAAAC...CGA-3'\n______________GAAUGGGG_______GAC_____GAAA__GAAUG_CG\n______________:\|\|\|:\|\|\|_______\|\|\|_____\|\|\|\|__\|\|\|\|\|_\|\|\n______________UUUAUCCC_______CUG_____CUUU__CUUAC_GC\n3'-UUU...CCAAC________CAUUUGU___UAAGU____A______U__CAUUA...UCG-5'\n_____________\|_____________________________________\|\n_____________64____________________________________27\n	184 -- 190	56 -- 62	-20.644 kcal/mol	5.44449 kcal/mol	6.29422 kcal/mol	182 216@LB@ \| \|@LB@5'-UGU...AUCAC AUUUUU UAU CG AAAAC...CGA-3'@LB@ GAAUGGGG GAC GAAA GAAUG CG@LB@ :\|\|\|:\|\|\| \|\|\| \|\|\|\| \|\|\|\|\| \|\|@LB@ UUUAUCCC CUG CUUU CUUAC GC@LB@3'-UUU...CCAAC CAUUUGU UAAGU A U CAUUA...UCG-5'@LB@ \| \|@LB@ 64 27@LB@@LB@@LB@Energy -8.91 kcal/mol@LB@Hybridization Energy -20.644 kcal/mol@LB@Unfolding Energy - mRNA 5.44449 kcal/mol@LB@Unfolding Energy - sRNA 6.29422 kcal/mol@LB@@LB@Position - mRNA 183 -- 215@LB@Position - sRNA 28 -- 63@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 56 -- 62@LB@
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@
54	0.006418	0.3902	b0946	zapC	-14.33	0.010402	184 -- 201	47 -- 63	FtsZ stabilizer	_____________183________________202\n_____________\|__________________\|\n5'-AUU...UUAUA_________AG_______UGCGA...GUU-3'\n______________GGGUAGGGG__AGGCAGA\n______________:::\|\|\|\|\|\|__\|::\|\|\|\|\n______________UUUAUCCCC__UUUGUCU\n3'-UUU...CCAAC_________A________GUAAG...UCG-5'\n_____________\|__________________\|\n_____________64_________________46\n	195 -- 201	47 -- 53	-19.5846 kcal/mol	3.17109 kcal/mol	2.08245 kcal/mol	183 202@LB@ \| \|@LB@5'-AUU...UUAUA AG UGCGA...GUU-3'@LB@ GGGUAGGGG AGGCAGA@LB@ :::\|\|\|\|\|\| \|::\|\|\|\|@LB@ UUUAUCCCC UUUGUCU@LB@3'-UUU...CCAAC A GUAAG...UCG-5'@LB@ \| \|@LB@ 64 46@LB@@LB@@LB@Energy -14.33 kcal/mol@LB@Hybridization Energy -19.5846 kcal/mol@LB@Unfolding Energy - mRNA 3.17109 kcal/mol@LB@Unfolding Energy - sRNA 2.08245 kcal/mol@LB@@LB@Position - mRNA 184 -- 201@LB@Position - sRNA 47 -- 63@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 47 -- 53@LB@
63	0.008816	0.4523	b3600	mtlD	-11.23	0.053963	184 -- 208	1 -- 23	mannitol-1-phosphate dehydrogenase NAD-dependent	_____________183_______________________209\n_____________\|_________________________\|\n5'-GUG...AACAU___UG_________ACU____A___AUUAC...AUC-3'\n______________UGA__AAGGUUAAU___AUGA_AGC\n______________\|:\|__\|\|:\|\|\|\|\|\|___\|\|\|\|_\|\|\|\n______________AUU__UUUCAAUUA___UACU_UCG\n3'-UUU...CCAUU___UA_________C______A___-5'\n_____________\|________________________\|\n_____________24_______________________1\n	191 -- 197	10 -- 16	-14.8386 kcal/mol	3.50103 kcal/mol	0.105066 kcal/mol	183 209@LB@ \| \|@LB@5'-GUG...AACAU UG ACU A AUUAC...AUC-3'@LB@ UGA AAGGUUAAU AUGA AGC@LB@ \|:\| \|\|:\|\|\|\|\|\| \|\|\|\| \|\|\|@LB@ AUU UUUCAAUUA UACU UCG@LB@3'-UUU...CCAUU UA C A -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -11.23 kcal/mol@LB@Hybridization Energy -14.8386 kcal/mol@LB@Unfolding Energy - mRNA 3.50103 kcal/mol@LB@Unfolding Energy - sRNA 0.105066 kcal/mol@LB@@LB@Position - mRNA 184 -- 208@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 10 -- 16@LB@
95	0.01574	0.5059	b2714	ascG	-10.13	0.091468	184 -- 220	14 -- 55	asc operon transcriptional repressor; prpBC operon repressor	_____________183________________________________________221\n_____________\|__________________________________________\|\n5'-AAA...UGCGU_____G_____________AU_______AC____CUG_____GGCGA...AAG-3'\n______________GUAAA_GGAU_____GAAA__GAUGACG__GAUG___GAAGU\n______________\|\|\|\|\|_:\|\|:_____\|\|\|\|__:\|\|\|\|\|\|__:\|\|:___:\|\|\|\|\n______________CAUUU_UCUG_____CUUU__UUACUGC__UUAU___UUUCA\n3'-UUU...AUCCC_____G____UAAGU____AC_______CA____UUA_____AUUAC...UCG-5'\n_____________\|__________________________________________\|\n_____________56_________________________________________13\n	200 -- 206	28 -- 34	-22.7561 kcal/mol	6.30192 kcal/mol	6.32604 kcal/mol	183 221@LB@ \| \|@LB@5'-AAA...UGCGU G AU AC CUG GGCGA...AAG-3'@LB@ GUAAA GGAU GAAA GAUGACG GAUG GAAGU@LB@ \|\|\|\|\| :\|\|: \|\|\|\| :\|\|\|\|\|\| :\|\|: :\|\|\|\|@LB@ CAUUU UCUG CUUU UUACUGC UUAU UUUCA@LB@3'-UUU...AUCCC G UAAGU AC CA UUA AUUAC...UCG-5'@LB@ \| \|@LB@ 56 13@LB@@LB@@LB@Energy -10.13 kcal/mol@LB@Hybridization Energy -22.7561 kcal/mol@LB@Unfolding Energy - mRNA 6.30192 kcal/mol@LB@Unfolding Energy - sRNA 6.32604 kcal/mol@LB@@LB@Position - mRNA 184 -- 220@LB@Position - sRNA 14 -- 55@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 28 -- 34@LB@
98	0.01586	0.5059	b1860	ruvB	-8.95	0.154425	184 -- 211	1 -- 30	ATP-dependent DNA helicase component of RuvABC resolvasome	_____________183_____________________________212\n_____________\|_______________________________\|\n5'-ACG...GCGCC___U__UG_______________U_______AGACC...GUC-3'\n______________GCG_UA__AGGUAAAG__GAUGA_UGA_AGC\n______________:\|\|_\|\|__\|::\|\|\|\|\|__:\|\|\|\|_\|\|\|_\|\|\|\n______________UGC_AU__UUUAUUUC__UUACU_ACU_UCG\n3'-UUU...CUUAC___C__UA________AA_________A___-5'\n_____________\|______________________________\|\n_____________31_____________________________1\n	193 -- 199	15 -- 21	-17.0174 kcal/mol	5.93551 kcal/mol	2.12822 kcal/mol	183 212@LB@ \| \|@LB@5'-ACG...GCGCC U UG U AGACC...GUC-3'@LB@ GCG UA AGGUAAAG GAUGA UGA AGC@LB@ :\|\| \|\| \|::\|\|\|\|\| :\|\|\|\| \|\|\| \|\|\|@LB@ UGC AU UUUAUUUC UUACU ACU UCG@LB@3'-UUU...CUUAC C UA AA A -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -8.95 kcal/mol@LB@Hybridization Energy -17.0174 kcal/mol@LB@Unfolding Energy - mRNA 5.93551 kcal/mol@LB@Unfolding Energy - sRNA 2.12822 kcal/mol@LB@@LB@Position - mRNA 184 -- 211@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 15 -- 21@LB@
159	0.02583	0.526	b2572	rseA	-12.83	0.023837	184 -- 236	1 -- 63	anti-sigma factor	_____________183_____________________________________________________________237\n_____________\|_______________________________________________________________\|\n5'-UCC...AUACU_____A_____U________G__________CA__UUUCCGCU____________________GAAAC...GGG-3'\n______________GGAUA_GGGUA__UAGGCAU_CAGAAA_GAA__AC______________UUAAUGG__AUGGC\n______________::\|\|\|_\|\|\|\|\|__:\|\|:\|\|\|_\|\|\|\|\|\|_\|\|\|__\|\|______________\|\|\|\|\|\|:__\|\|:\|\|\n______________UUUAU_CCCAU__GUCUGUA_GUCUUU_CUU__UG______________AAUUACU__UAUCG\n3'-UUU...CCAAC_____C_____UU_______A______A___AC__CCAUUAUUUAUUUC_______AC_____-5'\n_____________\|______________________________________________________________\|\n_____________64_____________________________________________________________1\n	225 -- 231	8 -- 14	-31.1691 kcal/mol	11.9981 kcal/mol	6.344 kcal/mol	183 237@LB@ \| \|@LB@5'-UCC...AUACU A U G CA UUUCCGCU GAAAC...GGG-3'@LB@ GGAUA GGGUA UAGGCAU CAGAAA GAA AC UUAAUGG AUGGC@LB@ ::\|\|\| \|\|\|\|\| :\|\|:\|\|\| \|\|\|\|\|\| \|\|\| \|\| \|\|\|\|\|\|: \|\|:\|\|@LB@ UUUAU CCCAU GUCUGUA GUCUUU CUU UG AAUUACU UAUCG@LB@3'-UUU...CCAAC C UU A A AC CCAUUAUUUAUUUC AC -5'@LB@ \| \|@LB@ 64 1@LB@@LB@@LB@Energy -12.83 kcal/mol@LB@Hybridization Energy -31.1691 kcal/mol@LB@Unfolding Energy - mRNA 11.9981 kcal/mol@LB@Unfolding Energy - sRNA 6.344 kcal/mol@LB@@LB@Position - mRNA 184 -- 236@LB@Position - sRNA 1 -- 63@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 8 -- 14@LB@
165	0.02655	0.526	b2388	glk	-7.68	0.259430	184 -- 233	1 -- 52	glucokinase	_____________183_____________________________________________________234\n_____________\|_______________________________________________________\|\n5'-CUA...ACUUU______G__GUU_____________AAA___UGCAUU_____C_______UG___GGCAC...AUU-3'\n______________AGCGGA_CA____GAA__GAAUGAC___GUA________AGU_GGUGAUG__GGC\n______________\|:\|:\|\|_\|\|____\|\|\|__\|\|\|\|\|\|\|___\|\|\|________\|\|\|_::\|\|\|\|\|__:\|\|\n______________UUGUCU_GU____CUU__CUUACUG___CAU________UCA_UUACUAC__UCG\n3'-UUU...CCCAU_________AAGU___UA_______C_____UAUUUAUU___A_______UA___-5'\n_____________\|______________________________________________________\|\n_____________53_____________________________________________________1\n	222 -- 228	6 -- 12	-28.455 kcal/mol	14.4434 kcal/mol	6.33555 kcal/mol	183 234@LB@ \| \|@LB@5'-CUA...ACUUU G GUU AAA UGCAUU C UG GGCAC...AUU-3'@LB@ AGCGGA CA GAA GAAUGAC GUA AGU GGUGAUG GGC@LB@ \|:\|:\|\| \|\| \|\|\| \|\|\|\|\|\|\| \|\|\| \|\|\| ::\|\|\|\|\| :\|\|@LB@ UUGUCU GU CUU CUUACUG CAU UCA UUACUAC UCG@LB@3'-UUU...CCCAU AAGU UA C UAUUUAUU A UA -5'@LB@ \| \|@LB@ 53 1@LB@@LB@@LB@Energy -7.68 kcal/mol@LB@Hybridization Energy -28.455 kcal/mol@LB@Unfolding Energy - mRNA 14.4434 kcal/mol@LB@Unfolding Energy - sRNA 6.33555 kcal/mol@LB@@LB@Position - mRNA 184 -- 233@LB@Position - sRNA 1 -- 52@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 6 -- 12@LB@
166	0.02659	0.526	b1580	rspB	-9.76	0.108040	184 -- 209	1 -- 29	putative Zn-dependent NAD(P)-binding oxidoreductase	_____________183___________________________210\n_____________\|_____________________________\|\n5'-AUG...GGAAC______G_______A_______AA_____AUAUU...UUG-3'\n______________UGGUAA_GAGUAAG__UAAUGA____AGC\n______________:\|\|\|\|\|_:\|:\|\|\|:__\|\|\|\|\|\|____\|\|\|\n______________GCCAUU_UUUAUUU__AUUACU____UCG\n3'-UUU...UUACU______A_______CA______ACUA___-5'\n_____________\|____________________________\|\n_____________30___________________________1\n	191 -- 197	16 -- 22	-16.0836 kcal/mol	4.192 kcal/mol	2.12711 kcal/mol	183 210@LB@ \| \|@LB@5'-AUG...GGAAC G A AA AUAUU...UUG-3'@LB@ UGGUAA GAGUAAG UAAUGA AGC@LB@ :\|\|\|\|\| :\|:\|\|\|: \|\|\|\|\|\| \|\|\|@LB@ GCCAUU UUUAUUU AUUACU UCG@LB@3'-UUU...UUACU A CA ACUA -5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -9.76 kcal/mol@LB@Hybridization Energy -16.0836 kcal/mol@LB@Unfolding Energy - mRNA 4.192 kcal/mol@LB@Unfolding Energy - sRNA 2.12711 kcal/mol@LB@@LB@Position - mRNA 184 -- 209@LB@Position - sRNA 1 -- 29@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 16 -- 22@LB@
4	6.512e-06	0.005344	b0929	ompF	-18.50	0.000749	185 -- 210	1 -- 33	outer membrane porin 1a (Ia;b;F)	_____________184_______________________________211\n_____________\|_________________________________\|\n5'-GUU...AAACC____G____________________________GCAAU...UAG-3'\n______________AUGA_GGUAAUAAAUA______AUGAUGA_AGC\n______________\|\|\|\|_\|\|\|\|\|\|\|\|\|\|\|______\|\|\|\|\|\|\|_\|\|\|\n______________UACU_CCAUUAUUUAU______UACUACU_UCG\n3'-UUU...UUACU____G___________UUCAAU_______A___-5'\n_____________\|________________________________\|\n_____________34_______________________________1\n	201 -- 207	5 -- 11	-27.1062 kcal/mol	3.13427 kcal/mol	5.47105 kcal/mol	184 211@LB@ \| \|@LB@5'-GUU...AAACC G GCAAU...UAG-3'@LB@ AUGA GGUAAUAAAUA AUGAUGA AGC@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|@LB@ UACU CCAUUAUUUAU UACUACU UCG@LB@3'-UUU...UUACU G UUCAAU A -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -18.50 kcal/mol@LB@Hybridization Energy -27.1062 kcal/mol@LB@Unfolding Energy - mRNA 3.13427 kcal/mol@LB@Unfolding Energy - sRNA 5.47105 kcal/mol@LB@@LB@Position - mRNA 185 -- 210@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 5 -- 11@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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