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
31	0.00291	0.3081	b1205	ychH	-11.03	0.059536	152 -- 163	53 -- 64	DUF2583 family putative inner membrane protein	_____________151__________164\n_____________\|____________\|\n5'-CAA...CAUAA____G_______UUCCC...UAC-3'\n______________GGAA_AGGGGUA\n______________\|:\|\|_\|\|\|\|\|\|\|\n______________CUUU_UCCCCAU\n3'-UUU...GCCAA____A_______UUGUC...UCG-5'\n_____________\|____________\|\n_____________65___________52\n	157 -- 163	53 -- 59	-13.5677 kcal/mol	2.46117 kcal/mol	0.0747267 kcal/mol	151 164@LB@ \| \|@LB@5'-CAA...CAUAA G UUCCC...UAC-3'@LB@ GGAA AGGGGUA@LB@ \|:\|\| \|\|\|\|\|\|\|@LB@ CUUU UCCCCAU@LB@3'-UUU...GCCAA A UUGUC...UCG-5'@LB@ \| \|@LB@ 65 52@LB@@LB@@LB@Energy -11.03 kcal/mol@LB@Hybridization Energy -13.5677 kcal/mol@LB@Unfolding Energy - mRNA 2.46117 kcal/mol@LB@Unfolding Energy - sRNA 0.0747267 kcal/mol@LB@@LB@Position - mRNA 152 -- 163@LB@Position - sRNA 53 -- 64@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 53 -- 59@LB@
32	0.003146	0.3086	b1553	rzpQ	-12.95	0.022283	187 -- 223	23 -- 60	Rz-like protein Qin prophage	_____________186______________________________________224\n_____________\|________________________________________\|\n5'-UAU...CCUGC______AUA______UGAA_____UAUUC___________UUUUC...GUG-3'\n______________UGGGGG___GAACAG____UCAGA________AUGGUGAU\n______________\|:\|\|\|\|___:\|\|\|\|\|____\|\|\|\|\|________\|:\|\|\|:\|\|\n______________AUCCCC___UUUGUC____AGUCU________UGCCAUUA\n3'-UUU...ACUUU______A________UGUA_____UUACUUAC________UUUAU...UCG-5'\n_____________\|________________________________________\|\n_____________61_______________________________________22\n	217 -- 223	23 -- 29	-27.4351 kcal/mol	8.1631 kcal/mol	6.31885 kcal/mol	186 224@LB@ \| \|@LB@5'-UAU...CCUGC AUA UGAA UAUUC UUUUC...GUG-3'@LB@ UGGGGG GAACAG UCAGA AUGGUGAU@LB@ \|:\|\|\|\| :\|\|\|\|\| \|\|\|\|\| \|:\|\|\|:\|\|@LB@ AUCCCC UUUGUC AGUCU UGCCAUUA@LB@3'-UUU...ACUUU A UGUA UUACUUAC UUUAU...UCG-5'@LB@ \| \|@LB@ 61 22@LB@@LB@@LB@Energy -12.95 kcal/mol@LB@Hybridization Energy -27.4351 kcal/mol@LB@Unfolding Energy - mRNA 8.1631 kcal/mol@LB@Unfolding Energy - sRNA 6.31885 kcal/mol@LB@@LB@Position - mRNA 187 -- 223@LB@Position - sRNA 23 -- 60@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 23 -- 29@LB@
33	0.003163	0.3086	b4372	holD	-10.86	0.064637	82 -- 98	44 -- 58	DNA polymerase III psi subunit	_____________81________________99\n_____________\|_________________\|\n5'-AGG...UUGCC_______AU________GGAAU...UCC-3'\n______________GGGGUAA__GCAGACAU\n______________\|\|\|\|\|\|\|__:\|\|\|\|\|\|\|\n______________CCCCAUU__UGUCUGUA\n3'-UUU...UUUAU_________________AGUCU...UCG-5'\n_____________\|_________________\|\n_____________59________________43\n	92 -- 98	44 -- 50	-21.4924 kcal/mol	4.96784 kcal/mol	5.66232 kcal/mol	81 99@LB@ \| \|@LB@5'-AGG...UUGCC AU GGAAU...UCC-3'@LB@ GGGGUAA GCAGACAU@LB@ \|\|\|\|\|\|\| :\|\|\|\|\|\|\|@LB@ CCCCAUU UGUCUGUA@LB@3'-UUU...UUUAU AGUCU...UCG-5'@LB@ \| \|@LB@ 59 43@LB@@LB@@LB@Energy -10.86 kcal/mol@LB@Hybridization Energy -21.4924 kcal/mol@LB@Unfolding Energy - mRNA 4.96784 kcal/mol@LB@Unfolding Energy - sRNA 5.66232 kcal/mol@LB@@LB@Position - mRNA 82 -- 98@LB@Position - sRNA 44 -- 58@LB@Position Seed - mRNA 92 -- 98@LB@Position Seed - sRNA 44 -- 50@LB@
34	0.003196	0.3086	b0896	dmsC	-10.70	0.070045	189 -- 235	4 -- 59	dimethyl sulfoxide reductase anaerobic subunit C	_____________188_______________________________________________________236\n_____________\|_________________________________________________________\|\n5'-CUG...CCCGA___A____UG__________________________________CCGC_________CUUCA...AAG-3'\n______________AGG_GGUG___AGAUG___GGAAGUGGAUGGC____AUGAAUGG______UGAUGAU\n______________\|\|\|_\|\|\|:___\|\|\|::___:\|\|\|:\|\|:\|\|\|:\|____\|\|:\|\|\|::______\|\|\|\|\|\|\|\n______________UCC_CCAU___UCUGU___UCUUUACUUACUG____UAUUUAUU______ACUACUA\n3'-UUU...CUUUA________UUG_____AAG_____________CCAU________UCAAUU_______UCG-5'\n_____________\|_________________________________________________________\|\n_____________60________________________________________________________3\n	229 -- 235	4 -- 10	-34.4804 kcal/mol	17.4476 kcal/mol	6.33761 kcal/mol	188 236@LB@ \| \|@LB@5'-CUG...CCCGA A UG CCGC CUUCA...AAG-3'@LB@ AGG GGUG AGAUG GGAAGUGGAUGGC AUGAAUGG UGAUGAU@LB@ \|\|\| \|\|\|: \|\|\|:: :\|\|\|:\|\|:\|\|\|:\| \|\|:\|\|\|:: \|\|\|\|\|\|\|@LB@ UCC CCAU UCUGU UCUUUACUUACUG UAUUUAUU ACUACUA@LB@3'-UUU...CUUUA UUG AAG CCAU UCAAUU UCG-5'@LB@ \| \|@LB@ 60 3@LB@@LB@@LB@Energy -10.70 kcal/mol@LB@Hybridization Energy -34.4804 kcal/mol@LB@Unfolding Energy - mRNA 17.4476 kcal/mol@LB@Unfolding Energy - sRNA 6.33761 kcal/mol@LB@@LB@Position - mRNA 189 -- 235@LB@Position - sRNA 4 -- 59@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 4 -- 10@LB@
35	0.003306	0.3101	b0551	quuD	-13.48	0.016718	188 -- 210	3 -- 24	DLP12 prophage; putative antitermination protein	_____________187_____________________211\n_____________\|_______________________\|\n5'-ACU...UUUUU_____GU_________C______UUCAG...GAU-3'\n______________GUGGA__AAGUUGAUG_GUGAUA\n______________:\|::\|__\|\|\|\|\|:\|\|\|_:\|\|\|\|\|\n______________UAUUU__UUCAAUUAC_UACUAU\n3'-UUU...GCCAU_____AU________________CG-5'\n_____________\|_______________________\|\n_____________25______________________2\n	197 -- 203	9 -- 15	-17.2545 kcal/mol	3.66311 kcal/mol	0.108279 kcal/mol	187 211@LB@ \| \|@LB@5'-ACU...UUUUU GU C UUCAG...GAU-3'@LB@ GUGGA AAGUUGAUG GUGAUA@LB@ :\|::\| \|\|\|\|\|:\|\|\| :\|\|\|\|\|@LB@ UAUUU UUCAAUUAC UACUAU@LB@3'-UUU...GCCAU AU CG-5'@LB@ \| \|@LB@ 25 2@LB@@LB@@LB@Energy -13.48 kcal/mol@LB@Hybridization Energy -17.2545 kcal/mol@LB@Unfolding Energy - mRNA 3.66311 kcal/mol@LB@Unfolding Energy - sRNA 0.108279 kcal/mol@LB@@LB@Position - mRNA 188 -- 210@LB@Position - sRNA 3 -- 24@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 9 -- 15@LB@
36	0.003415	0.3114	b1849	purT	-10.41	0.080237	8 -- 43	29 -- 56	phosphoribosylglycinamide formyltransferase 2	_____________7_____________________________________44\n_____________\|_____________________________________\|\n____5'-UUUUGCU_______________UCUCUUCGCCCUCAC_______UACGU...GUC-3'\n______________GGUAAAC_GACAUUU_______________GAAUGAC\n______________\|\|\|\|\|\|\|_\|\|\|\|\|\|:_______________\|\|\|\|\|\|\|\n______________CCAUUUG_CUGUAAG_______________CUUACUG\n3'-UUU...UAUCC_______U_______UCUUUA________________CCAUU...UCG-5'\n_____________\|_____________________________________\|\n_____________57____________________________________28\n	37 -- 43	29 -- 35	-21.896 kcal/mol	5.20104 kcal/mol	6.28612 kcal/mol	7 44@LB@ \| \|@LB@ 5'-UUUUGCU UCUCUUCGCCCUCAC UACGU...GUC-3'@LB@ GGUAAAC GACAUUU GAAUGAC@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|: \|\|\|\|\|\|\|@LB@ CCAUUUG CUGUAAG CUUACUG@LB@3'-UUU...UAUCC U UCUUUA CCAUU...UCG-5'@LB@ \| \|@LB@ 57 28@LB@@LB@@LB@Energy -10.41 kcal/mol@LB@Hybridization Energy -21.896 kcal/mol@LB@Unfolding Energy - mRNA 5.20104 kcal/mol@LB@Unfolding Energy - sRNA 6.28612 kcal/mol@LB@@LB@Position - mRNA 8 -- 43@LB@Position - sRNA 29 -- 56@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 29 -- 35@LB@
37	0.00362	0.3212	b4479	dgoR	-15.45	0.005416	239 -- 256	41 -- 57	D-galactonate catabolism operon transcriptional repressor	_____________238________________257\n_____________\|__________________\|\n5'-UUU...ACGCU___________U______CGGCA...AAC-3'\n______________GGGUAAACAGA_CGUUCA\n______________\|\|\|\|\|\|\|\|\|\|\|_\|:\|\|\|\|\n______________CCCAUUUGUCU_GUAAGU\n3'-UUU...UUAUC__________________CUUUA...UCG-5'\n_____________\|__________________\|\n_____________58_________________40\n	243 -- 249	47 -- 53	-24.0794 kcal/mol	2.38777 kcal/mol	6.24592 kcal/mol	238 257@LB@ \| \|@LB@5'-UUU...ACGCU U CGGCA...AAC-3'@LB@ GGGUAAACAGA CGUUCA@LB@ \|\|\|\|\|\|\|\|\|\|\| \|:\|\|\|\|@LB@ CCCAUUUGUCU GUAAGU@LB@3'-UUU...UUAUC CUUUA...UCG-5'@LB@ \| \|@LB@ 58 40@LB@@LB@@LB@Energy -15.45 kcal/mol@LB@Hybridization Energy -24.0794 kcal/mol@LB@Unfolding Energy - mRNA 2.38777 kcal/mol@LB@Unfolding Energy - sRNA 6.24592 kcal/mol@LB@@LB@Position - mRNA 239 -- 256@LB@Position - sRNA 41 -- 57@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 47 -- 53@LB@
38	0.003831	0.3287	b3739	atpI	-13.67	0.015109	253 -- 271	1 -- 16	ATP synthase membrane-bound accessory factor	_____________252_________________272\n_____________\|___________________\|\n5'-GAA...CGUUC_____CUG___________AAGUG...ACC-3'\n______________AGUUA___GUGGUGAUAGC\n______________\|\|\|\|\|___:\|\|:\|\|\|\|\|\|\|\n______________UCAAU___UACUACUAUCG\n3'-UUU...UUAUU___________________-5'\n_____________\|__________________\|\n_____________17_________________1\n	265 -- 271	1 -- 7	-18.239 kcal/mol	4.52285 kcal/mol	0.0492804 kcal/mol	252 272@LB@ \| \|@LB@5'-GAA...CGUUC CUG AAGUG...ACC-3'@LB@ AGUUA GUGGUGAUAGC@LB@ \|\|\|\|\| :\|\|:\|\|\|\|\|\|\|@LB@ UCAAU UACUACUAUCG@LB@3'-UUU...UUAUU -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -13.67 kcal/mol@LB@Hybridization Energy -18.239 kcal/mol@LB@Unfolding Energy - mRNA 4.52285 kcal/mol@LB@Unfolding Energy - sRNA 0.0492804 kcal/mol@LB@@LB@Position - mRNA 253 -- 271@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 1 -- 7@LB@
39	0.003905	0.3287	b3541	dppD	-12.54	0.027771	124 -- 154	26 -- 56	dipeptide/heme ABC transporter ATPas	_____________123_______________________________155\n_____________\|_________________________________\|\n5'-UUU...CUGAC_______U________ACCU_____________CUGCG...GCG-3'\n______________GGU__GC_GGCAUUUA____GAUGGGUGACGGU\n______________\|\|\|__:\|_\|:\|\|\|\|:\|____:\|\|\|::\|\|\|\|\|\|\|\n______________CCA__UG_CUGUAAGU____UUACUUACUGCCA\n3'-UUU...UAUCC___UU__U________CU_______________UUAUU...UCG-5'\n_____________\|_________________________________\|\n_____________57________________________________25\n	148 -- 154	26 -- 32	-28.6535 kcal/mol	9.81942 kcal/mol	6.29593 kcal/mol	123 155@LB@ \| \|@LB@5'-UUU...CUGAC U ACCU CUGCG...GCG-3'@LB@ GGU GC GGCAUUUA GAUGGGUGACGGU@LB@ \|\|\| :\| \|:\|\|\|\|:\| :\|\|\|::\|\|\|\|\|\|\|@LB@ CCA UG CUGUAAGU UUACUUACUGCCA@LB@3'-UUU...UAUCC UU U CU UUAUU...UCG-5'@LB@ \| \|@LB@ 57 25@LB@@LB@@LB@Energy -12.54 kcal/mol@LB@Hybridization Energy -28.6535 kcal/mol@LB@Unfolding Energy - mRNA 9.81942 kcal/mol@LB@Unfolding Energy - sRNA 6.29593 kcal/mol@LB@@LB@Position - mRNA 124 -- 154@LB@Position - sRNA 26 -- 56@LB@Position Seed - mRNA 148 -- 154@LB@Position Seed - sRNA 26 -- 32@LB@
40	0.004127	0.3349	b1659	ydhB	-12.78	0.024485	130 -- 177	1 -- 61	LysR family putative transcriptional regulator	_____________129_______________________________________________________________178\n_____________\|_________________________________________________________________\|\n5'-CGA...AAAGU______A_____AU_____________________________UU_______________C____UUCAA...UCA-3'\n______________GUAGGG_GUGAA__UAG_UGUU_____GUGAA__ACGGUAAUA___________UGAUGA_UGGU\n______________:\|\|\|\|\|_\|\|:\|\|__:\|\|_::\|\|_____:\|\|\|\|__\|\|\|\|\|\|\|\|\|___________\|\|\|\|\|\|_\|:\|:\n______________UAUCCC_CAUUU__GUC_GUAA_____UACUU__UGCCAUUAU___________ACUACU_AUCG\n3'-UUU...AACUU_________________U____GUCUU_____AC_________UUAUUUCAAUU___________-5'\n_____________\|________________________________________________________________\|\n_____________62_______________________________________________________________1\n	158 -- 164	22 -- 28	-31.01 kcal/mol	11.8895 kcal/mol	6.344 kcal/mol	129 178@LB@ \| \|@LB@5'-CGA...AAAGU A AU UU C UUCAA...UCA-3'@LB@ GUAGGG GUGAA UAG UGUU GUGAA ACGGUAAUA UGAUGA UGGU@LB@ :\|\|\|\|\| \|\|:\|\| :\|\| ::\|\| :\|\|\|\| \|\|\|\|\|\|\|\|\| \|\|\|\|\|\| \|:\|:@LB@ UAUCCC CAUUU GUC GUAA UACUU UGCCAUUAU ACUACU AUCG@LB@3'-UUU...AACUU U GUCUU AC UUAUUUCAAUU -5'@LB@ \| \|@LB@ 62 1@LB@@LB@@LB@Energy -12.78 kcal/mol@LB@Hybridization Energy -31.01 kcal/mol@LB@Unfolding Energy - mRNA 11.8895 kcal/mol@LB@Unfolding Energy - sRNA 6.344 kcal/mol@LB@@LB@Position - mRNA 130 -- 177@LB@Position - sRNA 1 -- 61@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 22 -- 28@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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