Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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
186	0.01069	0.1919	b1614	ydgA	-8.85	0.262719	182 -- 191	16 -- 25	DUF945 family protein		_____________181________192\n_____________\|__________\|\n5'-ACA...GAUUU__________AUAAU...UCG-3'\n______________CAUUUUAUGG\n______________\|\|\|\|\|\|\|\|\|\|\n______________GUAAAAUACC\n3'-UUU...CGAUC__________CAAUA...UCG-5'\n_____________\|__________\|\n_____________26_________15\n	185 -- 191	16 -- 22	-11.3536 kcal/mol	2.1555 kcal/mol	0.346409 kcal/mol	181 192@LB@ \| \|@LB@5'-ACA...GAUUU AUAAU...UCG-3'@LB@ CAUUUUAUGG@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ GUAAAAUACC@LB@3'-UUU...CGAUC CAAUA...UCG-5'@LB@ \| \|@LB@ 26 15@LB@@LB@@LB@Energy -8.85 kcal/mol@LB@Hybridization Energy -11.3536 kcal/mol@LB@Unfolding Energy - mRNA 2.1555 kcal/mol@LB@Unfolding Energy - sRNA 0.346409 kcal/mol@LB@@LB@Position - mRNA 182 -- 191@LB@Position - sRNA 16 -- 25@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 16 -- 22@LB@
150	0.00729	0.1634	b3184	yhbE	-11.29	0.093352	190 -- 235	1 -- 50	EamA family inner membrane putative transporter		_____________189_________________________________________________236\n_____________\|___________________________________________________\|\n5'-AAG...UUGCA____AUAC___A____AA_____A____GGCAU___CAUUC__________GCUCA...UGG-3'\n______________GGGA____GGU___UG__GCAGC_GGCA_____UGG________UUUUGGC\n______________:\|\|\|____\|\|\|___\|\|__:\|\|\|\|_:\|\|\|_____\|\|\|________\|\|\|::\|\|\n______________UCCU____CCA___AC__UGUCG_UCGU_____ACC________AAAGUCG\n3'-UUU...CCGAU____CCA____AGG__CA_____A____AAAAU___CAAUACAA_______-5'\n_____________\|__________________________________________________\|\n_____________51_________________________________________________1\n	229 -- 235	1 -- 7	-25.8939 kcal/mol	9.93833 kcal/mol	4.6634 kcal/mol	189 236@LB@ \| \|@LB@5'-AAG...UUGCA AUAC A AA A GGCAU CAUUC GCUCA...UGG-3'@LB@ GGGA GGU UG GCAGC GGCA UGG UUUUGGC@LB@ :\|\|\| \|\|\| \|\| :\|\|\|\| :\|\|\| \|\|\| \|\|\|::\|\|@LB@ UCCU CCA AC UGUCG UCGU ACC AAAGUCG@LB@3'-UUU...CCGAU CCA AGG CA A AAAAU CAAUACAA -5'@LB@ \| \|@LB@ 51 1@LB@@LB@@LB@Energy -11.29 kcal/mol@LB@Hybridization Energy -25.8939 kcal/mol@LB@Unfolding Energy - mRNA 9.93833 kcal/mol@LB@Unfolding Energy - sRNA 4.6634 kcal/mol@LB@@LB@Position - mRNA 190 -- 235@LB@Position - sRNA 1 -- 50@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 1 -- 7@LB@
82	0.002694	0.1082	b2474	tmcA	-11.34	0.091143	115 -- 147	1 -- 34	elongator methionine tRNA (ac4C34) acetyltransferase		_____________114________________________________148\n_____________\|__________________________________\|\n5'-GAU...AACGC__________UUAAACGU____UCGACAG_____GAUCC...UUG-3'\n______________UACAGCUGGU________GGUU________CGGC\n______________\|\|\|\|\|\|\|:\|:________\|\|\|\|________\|:\|\|\n______________AUGUCGAUCG________CCAA________GUCG\n3'-UUU...GGACC__________UAAAAUAC____UACAAAAA____-5'\n_____________\|_________________________________\|\n_____________35________________________________1\n	118 -- 124	25 -- 31	-23.7384 kcal/mol	10.9014 kcal/mol	1.49507 kcal/mol	114 148@LB@ \| \|@LB@5'-GAU...AACGC UUAAACGU UCGACAG GAUCC...UUG-3'@LB@ UACAGCUGGU GGUU CGGC@LB@ \|\|\|\|\|\|\|:\|: \|\|\|\| \|:\|\|@LB@ AUGUCGAUCG CCAA GUCG@LB@3'-UUU...GGACC UAAAAUAC UACAAAAA -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -11.34 kcal/mol@LB@Hybridization Energy -23.7384 kcal/mol@LB@Unfolding Energy - mRNA 10.9014 kcal/mol@LB@Unfolding Energy - sRNA 1.49507 kcal/mol@LB@@LB@Position - mRNA 115 -- 147@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 25 -- 31@LB@
17	0.0001135	0.02244	b3531	bcsZ	-11.80	0.072553	125 -- 136	14 -- 30	endo-1 4-D-glucanase		_____________124_______________137\n_____________\|_________________\|\n5'-UCA...AUAUU_________________ACUGU...AGG-3'\n______________GCUGGCA_____UGGGU\n______________\|\|\|:\|\|\|_____\|\|\|\|\|\n______________CGAUCGU_____ACCCA\n3'-UUU...CAUGU_______AAAAU_____AUACA...UCG-5'\n_____________\|_________________\|\n_____________31________________13\n	125 -- 131	24 -- 30	-17.2227 kcal/mol	4.01076 kcal/mol	1.40705 kcal/mol	124 137@LB@ \| \|@LB@5'-UCA...AUAUU ACUGU...AGG-3'@LB@ GCUGGCA UGGGU@LB@ \|\|\|:\|\|\| \|\|\|\|\|@LB@ CGAUCGU ACCCA@LB@3'-UUU...CAUGU AAAAU AUACA...UCG-5'@LB@ \| \|@LB@ 31 13@LB@@LB@@LB@Energy -11.80 kcal/mol@LB@Hybridization Energy -17.2227 kcal/mol@LB@Unfolding Energy - mRNA 4.01076 kcal/mol@LB@Unfolding Energy - sRNA 1.40705 kcal/mol@LB@@LB@Position - mRNA 125 -- 136@LB@Position - sRNA 14 -- 30@LB@Position Seed - mRNA 125 -- 131@LB@Position Seed - sRNA 24 -- 30@LB@
157	0.007972	0.1694	b4350	hsdR	-17.86	0.001148	15 -- 50	1 -- 35	endonuclease R Type I restriction enzyme		_____________14____________________________________51\n_____________\|_____________________________________\|\n5'-UAG...UCAUA_____UC__U___GAAUCA____AG____________UACUA...ACA-3'\n______________GUACA__CU_GCA_______GGU__AUGUUUUUCGGC\n______________\|\|\|\|\|__\|\|_\|\|\|_______\|\|\|__\|\|\|\|\|\|\|\|\|:\|\|\n______________CAUGU__GA_CGU_______CCA__UACAAAAAGUCG\n3'-UUU...AGGAC_____C___U___AAAAUAC___A_____________-5'\n_____________\|____________________________________\|\n_____________36___________________________________1\n	44 -- 50	1 -- 7	-27.1826 kcal/mol	7.83025 kcal/mol	1.49508 kcal/mol	14 51@LB@ \| \|@LB@5'-UAG...UCAUA UC U GAAUCA AG UACUA...ACA-3'@LB@ GUACA CU GCA GGU AUGUUUUUCGGC@LB@ \|\|\|\|\| \|\| \|\|\| \|\|\| \|\|\|\|\|\|\|\|\|:\|\|@LB@ CAUGU GA CGU CCA UACAAAAAGUCG@LB@3'-UUU...AGGAC C U AAAAUAC A -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -17.86 kcal/mol@LB@Hybridization Energy -27.1826 kcal/mol@LB@Unfolding Energy - mRNA 7.83025 kcal/mol@LB@Unfolding Energy - sRNA 1.49508 kcal/mol@LB@@LB@Position - mRNA 15 -- 50@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 44 -- 50@LB@Position Seed - sRNA 1 -- 7@LB@
22	0.0002072	0.03165	b2341	fadJ	-8.08	0.343546	182 -- 217	1 -- 44	enoyl-CoA hydratase/epimerase and isomerase/3-hydroxyacyl-CoA dehydrogenase		_____________181__________________________________________218\n_____________\|____________________________________________\|\n5'-CAU...GGCAA__________A________AAUA______AA____ACA______GUUUA...CGG-3'\n______________UGGUUCU_GG___GGC_GG______AUGG___AUG____UCAGC\n______________\|\|\|\|\|\|:_\|\|___:\|\|_:\|______\|\|\|\|___\|\|\|____\|\|\|\|\|\n______________ACCAAGG_CC___UCG_UC______UACC___UAC____AGUCG\n3'-UUU...CCUCC_______A__AUG___A__GUAAAA____CAA___AAAA_____-5'\n_____________\|___________________________________________\|\n_____________45__________________________________________1\n	182 -- 188	38 -- 44	-22.4043 kcal/mol	9.71146 kcal/mol	4.60934 kcal/mol	181 218@LB@ \| \|@LB@5'-CAU...GGCAA A AAUA AA ACA GUUUA...CGG-3'@LB@ UGGUUCU GG GGC GG AUGG AUG UCAGC@LB@ \|\|\|\|\|\|: \|\| :\|\| :\| \|\|\|\| \|\|\| \|\|\|\|\|@LB@ ACCAAGG CC UCG UC UACC UAC AGUCG@LB@3'-UUU...CCUCC A AUG A GUAAAA CAA AAAA -5'@LB@ \| \|@LB@ 45 1@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -22.4043 kcal/mol@LB@Unfolding Energy - mRNA 9.71146 kcal/mol@LB@Unfolding Energy - sRNA 4.60934 kcal/mol@LB@@LB@Position - mRNA 182 -- 217@LB@Position - sRNA 1 -- 44@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 38 -- 44@LB@
129	0.005449	0.142	b2502	ppx	-11.35	0.090652	145 -- 164	17 -- 36	exopolyphosphatase		_____________144__________________165\n_____________\|____________________\|\n5'-GGC...GUACG__C__________A______ACUAC...GUG-3'\n______________GG_GCAGUUGGCG_UUUAUG\n______________\|\|_:\|\|\|:\|:\|\|:_\|\|\|\|\|\|\n______________CC_UGUCGAUCGU_AAAUAC\n3'-UUU...AAGGA__A__________A______CCAAU...UCG-5'\n_____________\|____________________\|\n_____________37___________________16\n	151 -- 157	24 -- 30	-21.6291 kcal/mol	8.82633 kcal/mol	1.44969 kcal/mol	144 165@LB@ \| \|@LB@5'-GGC...GUACG C A ACUAC...GUG-3'@LB@ GG GCAGUUGGCG UUUAUG@LB@ \|\| :\|\|\|:\|:\|\|: \|\|\|\|\|\|@LB@ CC UGUCGAUCGU AAAUAC@LB@3'-UUU...AAGGA A A CCAAU...UCG-5'@LB@ \| \|@LB@ 37 16@LB@@LB@@LB@Energy -11.35 kcal/mol@LB@Hybridization Energy -21.6291 kcal/mol@LB@Unfolding Energy - mRNA 8.82633 kcal/mol@LB@Unfolding Energy - sRNA 1.44969 kcal/mol@LB@@LB@Position - mRNA 145 -- 164@LB@Position - sRNA 17 -- 36@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 24 -- 30@LB@
61	0.001594	0.08781	b1905	ftnA	-13.68	0.025904	280 -- 298	27 -- 44	ferritin iron storage protein (cytoplasmic)		_____________279_________________299\n_____________\|___________________\|\n5'-CAU...GCAAA__A_CG_____________UC-3'\n______________UG_G__CCUGGUGCAGCUA\n______________\|\|_\|__\|\|\|\|\|\|:\|\|\|\|\|\|\n______________AC_C__GGACCAUGUCGAU\n3'-UUU...CCUCC____AA_____________CGUAA...UCG-5'\n_____________\|___________________\|\n_____________45__________________26\n	292 -- 298	27 -- 33	-25.294 kcal/mol	7.30746 kcal/mol	4.30747 kcal/mol	279 299@LB@ \| \|@LB@5'-CAU...GCAAA A CG UC-3'@LB@ UG G CCUGGUGCAGCUA@LB@ \|\| \| \|\|\|\|\|\|:\|\|\|\|\|\|@LB@ AC C GGACCAUGUCGAU@LB@3'-UUU...CCUCC AA CGUAA...UCG-5'@LB@ \| \|@LB@ 45 26@LB@@LB@@LB@Energy -13.68 kcal/mol@LB@Hybridization Energy -25.294 kcal/mol@LB@Unfolding Energy - mRNA 7.30746 kcal/mol@LB@Unfolding Energy - sRNA 4.30747 kcal/mol@LB@@LB@Position - mRNA 280 -- 298@LB@Position - sRNA 27 -- 44@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 27 -- 33@LB@
99	0.003591	0.1219	b0533	sfmH	-7.90	0.364135	113 -- 140	1 -- 34	FimA homolog function unknown	b3145 b0941	_____________112________________________________141\n_____________\|__________________________________\|\n5'-GAC...AAGCU______A___CGUCACU_________________AGUUU...AUA-3'\n______________UACAGC_AGC_________GUUA____UUUCGGC\n______________\|\|\|\|\|\|_\|\|\|_________\|\|\|\|____\|\|\|\|:\|\|\n______________AUGUCG_UCG_________CAAU____AAAGUCG\n3'-UUU...GGACC______A___UAAAAUACC____ACAA_______-5'\n_____________\|_________________________________\|\n_____________35________________________________1\n	134 -- 140	1 -- 7	-18.6412 kcal/mol	9.24123 kcal/mol	1.49507 kcal/mol	112 141@LB@ \| \|@LB@5'-GAC...AAGCU A CGUCACU AGUUU...AUA-3'@LB@ UACAGC AGC GUUA UUUCGGC@LB@ \|\|\|\|\|\| \|\|\| \|\|\|\| \|\|\|\|:\|\|@LB@ AUGUCG UCG CAAU AAAGUCG@LB@3'-UUU...GGACC A UAAAAUACC ACAA -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -7.90 kcal/mol@LB@Hybridization Energy -18.6412 kcal/mol@LB@Unfolding Energy - mRNA 9.24123 kcal/mol@LB@Unfolding Energy - sRNA 1.49507 kcal/mol@LB@@LB@Position - mRNA 113 -- 140@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 1 -- 7@LB@
151	0.007423	0.1652	b2895	fldB	-9.53	0.202764	191 -- 224	1 -- 31	flavodoxin 2		_____________190__________________________________225\n_____________\|____________________________________\|\n5'-CGG...CGAGA____UA____AUGAA_______CU_______A____UCCAG...AUA-3'\n______________AGCU__CGUU_____UAUGGGU____UUUUU_CGGU\n______________\|\|\|\|__\|:\|\|_____\|\|\|\|\|\|\|____\|\|\|\|\|_\|:\|:\n______________UCGA__GUAA_____AUACCCA____AAAAA_GUCG\n3'-UUU...CCAUG____UC____A___________AUAC__________-5'\n_____________\|___________________________________\|\n_____________32__________________________________1\n	206 -- 212	14 -- 20	-17.4845 kcal/mol	6.4701 kcal/mol	1.48722 kcal/mol	190 225@LB@ \| \|@LB@5'-CGG...CGAGA UA AUGAA CU A UCCAG...AUA-3'@LB@ AGCU CGUU UAUGGGU UUUUU CGGU@LB@ \|\|\|\| \|:\|\| \|\|\|\|\|\|\| \|\|\|\|\| \|:\|:@LB@ UCGA GUAA AUACCCA AAAAA GUCG@LB@3'-UUU...CCAUG UC A AUAC -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -9.53 kcal/mol@LB@Hybridization Energy -17.4845 kcal/mol@LB@Unfolding Energy - mRNA 6.4701 kcal/mol@LB@Unfolding Energy - sRNA 1.48722 kcal/mol@LB@@LB@Position - mRNA 191 -- 224@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 14 -- 20@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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