Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
37	0.00305	0.2773	b4084	alsK	-13.69	0.050122	28 -- 80	50 -- 101	D-allose kinase	_____________27__________________________________________________________81\n_____________\|___________________________________________________________\|\n5'-GCG...UACGA_____AG________G_________________________A__AAAAA___A_G____CAGGG...AAA-3'\n______________AAUUG__GU_GGACG_UU__CC__UGCAACCAG_GCAACUU_CG_____CUG_U_GCGG\n______________\|\|\|:\|__\|\|_\|\|\|\|\|_\|\|__\|\|__:\|\|\|\|\|\|\|\|_:\|\|\|\|\|\|_\|\|_____\|\|\|_\|_\|\|\|\|\n______________UUAGC__CA_CCUGC_AA__GG__GCGUUGGUC_UGUUGAA_GC_____GAC_A_CGCC\n3'-UUU...ACCAA_____AA__C_____G__UU__UU_________G____________________G____AUUUU...UAG-5'\n_____________\|___________________________________________________________\|\n_____________102_________________________________________________________49\n	56 -- 62	61 -- 67	-47.5504 kcal/mol	15.3524 kcal/mol	25.4279 kcal/mol	27 81@LB@ \| \|@LB@5'-GCG...UACGA AG G A AAAAA A G CAGGG...AAA-3'@LB@ AAUUG GU GGACG UU CC UGCAACCAG GCAACUU CG CUG U GCGG@LB@ \|\|\|:\| \|\| \|\|\|\|\| \|\| \|\| :\|\|\|\|\|\|\|\| :\|\|\|\|\|\| \|\| \|\|\| \| \|\|\|\|@LB@ UUAGC CA CCUGC AA GG GCGUUGGUC UGUUGAA GC GAC A CGCC@LB@3'-UUU...ACCAA AA C G UU UU G G AUUUU...UAG-5'@LB@ \| \|@LB@ 102 49@LB@@LB@@LB@Energy -13.69 kcal/mol@LB@Hybridization Energy -47.5504 kcal/mol@LB@Unfolding Energy - mRNA 15.3524 kcal/mol@LB@Unfolding Energy - sRNA 25.4279 kcal/mol@LB@@LB@Position - mRNA 28 -- 80@LB@Position - sRNA 50 -- 101@LB@Position Seed - mRNA 56 -- 62@LB@Position Seed - sRNA 61 -- 67@LB@
193	0.0225	0.3833	b3751	rbsB	-14.76	0.030308	38 -- 56	74 -- 93	D-ribose ABC transporter periplasmic binding protein; ribose chemotaxis receptor	_____________37________________________________________________57\n_____________\|_________________________________________________\|\n___5'-GCGGUACG_____GG______GAAAA_____CA___U____________________UUAAU...UCU-3'\n______________AGUCU__CGGGCG_____GGUCG__UUG_UGGGACGUU_GAUCGGCGCA\n______________\|\|\|\|:__\|::\|\|:_____::\|\|\|__\|\|\|_\|\|\|\|\|\|\|:\|_:\|:\|::\|\|\|\|\n______________UCAGG__GUUCGU_____UUAGC__AAC_ACCCUGCGA_UUGGUUGCGU\n3'-UUU...CGUAG_____AA______ACCAA____________________A__________UGGUC...UAG-5'\n_____________\|_________________________________________________\|\n_____________94________________________________________________73\n	40 -- 46	85 -- 91	-47.7546 kcal/mol	17.619 kcal/mol	19.1533 kcal/mol	37 57@LB@ \| \|@LB@ 5'-GCGGUACG GG GAAAA CA U UUAAU...UCU-3'@LB@ AGUCU CGGGCG GGUCG UUG UGGGACGUU GAUCGGCGCA@LB@ \|\|\|\|: \|::\|\|: ::\|\|\| \|\|\| \|\|\|\|\|\|\|:\| :\|:\|::\|\|\|\|@LB@ UCAGG GUUCGU UUAGC AAC ACCCUGCGA UUGGUUGCGU@LB@3'-UUU...CGUAG AA ACCAA A UGGUC...UAG-5'@LB@ \| \|@LB@ 94 73@LB@@LB@@LB@Energy -14.76 kcal/mol@LB@Hybridization Energy -47.7546 kcal/mol@LB@Unfolding Energy - mRNA 17.619 kcal/mol@LB@Unfolding Energy - sRNA 19.1533 kcal/mol@LB@@LB@Position - mRNA 38 -- 56@LB@Position - sRNA 74 -- 93@LB@Position Seed - mRNA 40 -- 46@LB@Position Seed - sRNA 85 -- 91@LB@
63	0.006154	0.3261	b3750	rbsC	-15.65	0.019915	89 -- 120	139 -- 174	D-ribose ABC transporter permease	_____________88___________________________________121\n_____________\|____________________________________\|\n5'-GAU...UCAUC___________A_______UC_____GG________UACUC...UCU-3'\n______________GUCAUGCAUGA___GGGCA__UCAGC____GGAAUU\n______________\|\|\|\|::\|\|\|\|\|___:\|\|\|\|__\|\|\|:\|____:\|\|\|\|\|\n______________CAGUGUGUACU___UCCGU__AGUUG____UCUUAA\n3'-UUU...UGAGU___________ACG_____UC_____AAAG______CGCCA...UAG-5'\n_____________\|____________________________________\|\n_____________175__________________________________138\n	91 -- 97	166 -- 172	-33.4294 kcal/mol	9.19626 kcal/mol	8.8011 kcal/mol	88 121@LB@ \| \|@LB@5'-GAU...UCAUC A UC GG UACUC...UCU-3'@LB@ GUCAUGCAUGA GGGCA UCAGC GGAAUU@LB@ \|\|\|\|::\|\|\|\|\| :\|\|\|\| \|\|\|:\| :\|\|\|\|\|@LB@ CAGUGUGUACU UCCGU AGUUG UCUUAA@LB@3'-UUU...UGAGU ACG UC AAAG CGCCA...UAG-5'@LB@ \| \|@LB@ 175 138@LB@@LB@@LB@Energy -15.65 kcal/mol@LB@Hybridization Energy -33.4294 kcal/mol@LB@Unfolding Energy - mRNA 9.19626 kcal/mol@LB@Unfolding Energy - sRNA 8.8011 kcal/mol@LB@@LB@Position - mRNA 89 -- 120@LB@Position - sRNA 139 -- 174@LB@Position Seed - mRNA 91 -- 97@LB@Position Seed - sRNA 166 -- 172@LB@
35	0.002845	0.2736	b3887	dtd	-14.98	0.027287	55 -- 74	191 -- 211	D-tyr-tRNA(Tyr) deacylase	_____________54____________________75\n_____________\|_____________________\|\n5'-GGA...UCAUU______G______________CCCCA...UCG-3'\n______________UAUGGU_UGCUGGCGG_UGAU\n______________\|\|\|::\|_\|\|\|\|\|\|\|\|\|_\|\|\|\|\n______________AUAUUA_ACGACCGCC_ACUA\n3'-UUU...CGUCC______G_________C____AAAUG...UAG-5'\n_____________\|_____________________\|\n_____________212___________________190\n	64 -- 70	196 -- 202	-27.702 kcal/mol	6.2401 kcal/mol	11.5765 kcal/mol	54 75@LB@ \| \|@LB@5'-GGA...UCAUU G CCCCA...UCG-3'@LB@ UAUGGU UGCUGGCGG UGAU@LB@ \|\|\|::\| \|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ AUAUUA ACGACCGCC ACUA@LB@3'-UUU...CGUCC G C AAAUG...UAG-5'@LB@ \| \|@LB@ 212 190@LB@@LB@@LB@Energy -14.98 kcal/mol@LB@Hybridization Energy -27.702 kcal/mol@LB@Unfolding Energy - mRNA 6.2401 kcal/mol@LB@Unfolding Energy - sRNA 11.5765 kcal/mol@LB@@LB@Position - mRNA 55 -- 74@LB@Position - sRNA 191 -- 211@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 196 -- 202@LB@
79	0.008119	0.3458	b0945	pyrD	-11.48	0.141710	30 -- 41	191 -- 202	dihydro-orotate oxidase FMN-linked	_____________29______________________42\n_____________\|_______________________\|\n5'-UGU...AGCAA_____________A___GA____CGU-3'\n______________UUACGCCG_UAUU_CAG__ACGC\n______________\|\|\|\|:\|\|:_\|\|:\|_\|\|\|__\|\|:\|\n______________AAUGUGGU_AUGA_GUC__UGUG\n3'-UUU...ACUAA________U________AG____UACUA...UAG-5'\n_____________\|_______________________\|\n_____________203_____________________190\n	277 -- 283	182 -- 188	-20.4941 kcal/mol	3.55802 kcal/mol	4.91485 kcal/mol	29 42@LB@ \| \|@LB@5'-UGU...AGCAA A GA CGU-3'@LB@ UUACGCCG UAUU CAG ACGC@LB@ \|\|\|\|:\|\|: \|\|:\| \|\|\| \|\|:\|@LB@ AAUGUGGU AUGA GUC UGUG@LB@3'-UUU...ACUAA U AG UACUA...UAG-5'@LB@ \| \|@LB@ 203 190@LB@@LB@@LB@Energy -11.48 kcal/mol@LB@Hybridization Energy -20.4941 kcal/mol@LB@Unfolding Energy - mRNA 3.55802 kcal/mol@LB@Unfolding Energy - sRNA 4.91485 kcal/mol@LB@@LB@Position - mRNA 30 -- 41@LB@Position - sRNA 191 -- 202@LB@Position Seed - mRNA 277 -- 283@LB@Position Seed - sRNA 182 -- 188@LB@
131	0.01426	0.3575	b0048	folA	-12.08	0.107221	135 -- 211	115 -- 187	dihydrofolate reductase	_____________134_________212\n_____________\|___________\|\n5'-UCA...UUGUU___________GUAAU...GCA-3'\n______________UUUGUUUCAUU\n______________:\|\|\|:\|\|\|\|\|:\n______________GAACGAAGUAG\n3'-UUU...UGGGG___________-5'\n_____________\|__________\|\n_____________188________115\n	56 -- 62	1 -- 7	-10.5455 kcal/mol	1.7602 kcal/mol	1.03329 kcal/mol	134 212@LB@ \| \|@LB@5'-UCA...UUGUU GUAAU...GCA-3'@LB@ UUUGUUUCAUU@LB@ :\|\|\|:\|\|\|\|\|:@LB@ GAACGAAGUAG@LB@3'-UUU...UGGGG -5'@LB@ \| \|@LB@ 188 115@LB@@LB@@LB@Energy -12.08 kcal/mol@LB@Hybridization Energy -10.5455 kcal/mol@LB@Unfolding Energy - mRNA 1.7602 kcal/mol@LB@Unfolding Energy - sRNA 1.03329 kcal/mol@LB@@LB@Position - mRNA 135 -- 211@LB@Position - sRNA 115 -- 187@LB@Position Seed - mRNA 56 -- 62@LB@Position Seed - sRNA 1 -- 7@LB@
138	0.01487	0.3575	b3771	ilvD	-15.83	0.018324	35 -- 66	67 -- 98	dihydroxyacid dehydratase	_____________34______67\n_____________\|_______\|\n5'-GCG...AAAAA_______GCACG...GUA-3'\n______________UGGGACG\n______________\|\|\|\|\|\|\|\n______________ACCCUGC\n3'-UUU...GCAAC_______GAAUU...UAG-5'\n_____________\|_______\|\n_____________99______66\n	147 -- 153	87 -- 93	-12.7493 kcal/mol	2.26202 kcal/mol	4.21173 kcal/mol	34 67@LB@ \| \|@LB@5'-GCG...AAAAA GCACG...GUA-3'@LB@ UGGGACG@LB@ \|\|\|\|\|\|\|@LB@ ACCCUGC@LB@3'-UUU...GCAAC GAAUU...UAG-5'@LB@ \| \|@LB@ 99 66@LB@@LB@@LB@Energy -15.83 kcal/mol@LB@Hybridization Energy -12.7493 kcal/mol@LB@Unfolding Energy - mRNA 2.26202 kcal/mol@LB@Unfolding Energy - sRNA 4.21173 kcal/mol@LB@@LB@Position - mRNA 35 -- 66@LB@Position - sRNA 67 -- 98@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 87 -- 93@LB@
155	0.01733	0.3749	b3542	dppC	-14.36	0.036537	40 -- 62	74 -- 93	dipeptide/heme ABC transporter permease	_____________39_______________________________________________________63\n_____________\|________________________________________________________\|\n5'-GGG...UCGUC____U__U___C__________UA___C_____GA_______C_____________AGAAG...UCG-3'\n______________AACU_GC_GGU__GAUCUGCUG__CGG_GUGGU___AC_CCG_GUAUUC_GUCAUA\n______________\|\|\|:_\|\|_\|\|\|__:\|\|\|\|\|\|\|\|__\|\|\|_\|\|\|:\|___\|\|_\|\|:_:\|\|:\|\|_\|\|\|\|:\|\n______________UUGG_CG_CCA__UUAGACGAC__GCC_CACUA___UG_GGU_UAUGAG_CAGUGU\n_____3'-UUUUUU____U__U___UA_________C__________AAA__U__________U______GUACU...UAG-5'\n_____________\|________________________________________________________\|\n_____________94_______________________________________________________73\n	146 -- 152	200 -- 206	-46.3163 kcal/mol	15.5571 kcal/mol	18.3074 kcal/mol	39 63@LB@ \| \|@LB@5'-GGG...UCGUC U U C UA C GA C AGAAG...UCG-3'@LB@ AACU GC GGU GAUCUGCUG CGG GUGGU AC CCG GUAUUC GUCAUA@LB@ \|\|\|: \|\| \|\|\| :\|\|\|\|\|\|\|\| \|\|\| \|\|\|:\| \|\| \|\|: :\|\|:\|\| \|\|\|\|:\|@LB@ UUGG CG CCA UUAGACGAC GCC CACUA UG GGU UAUGAG CAGUGU@LB@ 3'-UUUUUU U U UA C AAA U U GUACU...UAG-5'@LB@ \| \|@LB@ 94 73@LB@@LB@@LB@Energy -14.36 kcal/mol@LB@Hybridization Energy -46.3163 kcal/mol@LB@Unfolding Energy - mRNA 15.5571 kcal/mol@LB@Unfolding Energy - sRNA 18.3074 kcal/mol@LB@@LB@Position - mRNA 40 -- 62@LB@Position - sRNA 74 -- 93@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 200 -- 206@LB@
43	0.003721	0.2912	b3232	zapE	-10.85	0.189153	236 -- 256	70 -- 90	divisome ATPase	_____________235___________257\n_____________\|_____________\|\n5'-AGG...AACGG____UU_______AACCG...AAA-3'\n______________CCUU__UUUCGUC\n______________\|\|\|\|__:\|\|\|:\|\|\n______________GGAA__GAAGUAG\n3'-UUU...GUGGG____C________-5'\n_____________\|____________\|\n_____________91___________70\n	146 -- 152	1 -- 7	-9.27362 kcal/mol	0.691484 kcal/mol	1.04836 kcal/mol	235 257@LB@ \| \|@LB@5'-AGG...AACGG UU AACCG...AAA-3'@LB@ CCUU UUUCGUC@LB@ \|\|\|\| :\|\|\|:\|\|@LB@ GGAA GAAGUAG@LB@3'-UUU...GUGGG C -5'@LB@ \| \|@LB@ 91 70@LB@@LB@@LB@Energy -10.85 kcal/mol@LB@Hybridization Energy -9.27362 kcal/mol@LB@Unfolding Energy - mRNA 0.691484 kcal/mol@LB@Unfolding Energy - sRNA 1.04836 kcal/mol@LB@@LB@Position - mRNA 236 -- 256@LB@Position - sRNA 70 -- 90@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 1 -- 7@LB@
127	0.01385	0.3575	b3832	rmuC	-11.83	0.120260	236 -- 246	193 -- 203	DNA recombination protein	_____________235____________________________________________________________247\n_____________\|______________________________________________________________\|\n5'-AAA...UUGUA________AUUC___UUU_____________GUU__G______AGGC_______AUU_____AUCAU...AGC-3'\n______________CAG_CACA____UAU___GUGCGGGUAAGUU___GC__UCAGG____GUUGUGG___UCUCA\n______________\|\|\|_\|\|\|\|____:\|\|___:\|\|\|:\|\|:\|\|\|\|:___:\|__\|\|\|\|:____:\|\|\|:\|\|___\|\|:\|\|\n______________GUC_GUGU____GUA___UACGUCCGUUCAG___UG__AGUCU____UAACGCC___AGGGU\n3'-UUU...UAUGA___A___________C_______________U____AA________________AGU_____GACGU...UAG-5'\n_____________\|______________________________________________________________\|\n_____________204____________________________________________________________192\n	198 -- 204	135 -- 141	-42.9883 kcal/mol	19.1075 kcal/mol	15.6146 kcal/mol	235 247@LB@ \| \|@LB@5'-AAA...UUGUA AUUC UUU GUU G AGGC AUU AUCAU...AGC-3'@LB@ CAG CACA UAU GUGCGGGUAAGUU GC UCAGG GUUGUGG UCUCA@LB@ \|\|\| \|\|\|\| :\|\| :\|\|\|:\|\|:\|\|\|\|: :\| \|\|\|\|: :\|\|\|:\|\| \|\|:\|\|@LB@ GUC GUGU GUA UACGUCCGUUCAG UG AGUCU UAACGCC AGGGU@LB@3'-UUU...UAUGA A C U AA AGU GACGU...UAG-5'@LB@ \| \|@LB@ 204 192@LB@@LB@@LB@Energy -11.83 kcal/mol@LB@Hybridization Energy -42.9883 kcal/mol@LB@Unfolding Energy - mRNA 19.1075 kcal/mol@LB@Unfolding Energy - sRNA 15.6146 kcal/mol@LB@@LB@Position - mRNA 236 -- 246@LB@Position - sRNA 193 -- 203@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 135 -- 141@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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