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
179	0.01003	0.1882	b0619	citA	-9.15	0.235039	224 -- 237	20 -- 33	sensory histidine kinase in two-component regulatory system with CitB	_____________223____________238\n_____________\|______________\|\n5'-CAU...AAUAA______U_______UCCAA...UCA-3'\n______________ACAGUU_GCAUUUU\n______________\|\|\|\|:\|_\|\|\|\|\|\|\|\n______________UGUCGA_CGUAAAA\n3'-UUU...GACCA______U_______UACCC...UCG-5'\n_____________\|______________\|\n_____________34_____________19\n	231 -- 237	20 -- 26	-13.7934 kcal/mol	3.21006 kcal/mol	1.43447 kcal/mol	223 238@LB@ \| \|@LB@5'-CAU...AAUAA U UCCAA...UCA-3'@LB@ ACAGUU GCAUUUU@LB@ \|\|\|\|:\| \|\|\|\|\|\|\|@LB@ UGUCGA CGUAAAA@LB@3'-UUU...GACCA U UACCC...UCG-5'@LB@ \| \|@LB@ 34 19@LB@@LB@@LB@Energy -9.15 kcal/mol@LB@Hybridization Energy -13.7934 kcal/mol@LB@Unfolding Energy - mRNA 3.21006 kcal/mol@LB@Unfolding Energy - sRNA 1.43447 kcal/mol@LB@@LB@Position - mRNA 224 -- 237@LB@Position - sRNA 20 -- 33@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 20 -- 26@LB@
195	0.01134	0.1946	b0633	rlpA	-8.12	0.339483	43 -- 55	25 -- 37	septal ring protein suppressor of prc minor lipoprotein	_____________42____________56\n_____________\|_____________\|\n5'-CGG...AAUAU_________A___GGUAU...CUG-3'\n______________UGGUAUGGU_AGC\n______________\|\|\|\|\|::\|:_\|\|\|\n______________ACCAUGUCG_UCG\n3'-UUU...CAAGG_________A___UAAAA...UCG-5'\n_____________\|_____________\|\n_____________38____________24\n	45 -- 51	29 -- 35	-15.087 kcal/mol	4.33932 kcal/mol	2.62824 kcal/mol	42 56@LB@ \| \|@LB@5'-CGG...AAUAU A GGUAU...CUG-3'@LB@ UGGUAUGGU AGC@LB@ \|\|\|\|\|::\|: \|\|\|@LB@ ACCAUGUCG UCG@LB@3'-UUU...CAAGG A UAAAA...UCG-5'@LB@ \| \|@LB@ 38 24@LB@@LB@@LB@Energy -8.12 kcal/mol@LB@Hybridization Energy -15.087 kcal/mol@LB@Unfolding Energy - mRNA 4.33932 kcal/mol@LB@Unfolding Energy - sRNA 2.62824 kcal/mol@LB@@LB@Position - mRNA 43 -- 55@LB@Position - sRNA 25 -- 37@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 29 -- 35@LB@
46	0.00106	0.07744	b3234	degQ	-13.26	0.033170	226 -- 262	1 -- 35	serine endoprotease periplasmic	_____________225____________________________________263\n_____________\|______________________________________\|\n5'-CUG...GUUGA______________AAG___C______ACUCUC_____GUCAU...UUG-3'\n______________GUGCA_UUAGCGUU___UGU_GGGUUA______UCGGC\n______________\|\|:\|\|_:\|\|\|\|:\|\|___\|:\|_\|\|\|\|\|\|______\|\|:\|\|\n______________CAUGU_GAUCGUAA___AUA_CCCAAU______AGUCG\n3'-UUU...AGGAC_____C________A____________ACAAAA_____-5'\n_____________\|_____________________________________\|\n_____________36____________________________________1\n	232 -- 238	22 -- 28	-28.0432 kcal/mol	13.2904 kcal/mol	1.49508 kcal/mol	225 263@LB@ \| \|@LB@5'-CUG...GUUGA AAG C ACUCUC GUCAU...UUG-3'@LB@ GUGCA UUAGCGUU UGU GGGUUA UCGGC@LB@ \|\|:\|\| :\|\|\|\|:\|\| \|:\| \|\|\|\|\|\| \|\|:\|\|@LB@ CAUGU GAUCGUAA AUA CCCAAU AGUCG@LB@3'-UUU...AGGAC C A ACAAAA -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -13.26 kcal/mol@LB@Hybridization Energy -28.0432 kcal/mol@LB@Unfolding Energy - mRNA 13.2904 kcal/mol@LB@Unfolding Energy - sRNA 1.49508 kcal/mol@LB@@LB@Position - mRNA 226 -- 262@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 22 -- 28@LB@
6	7.051e-06	0.00395	b1213	ychQ	-11.22	0.096653	74 -- 98	15 -- 40	SIRB family inner membrane protein	_____________73___________________________99\n_____________\|____________________________\|\n5'-GAC...UCUGC______AAC__________GCA______CGAAG...AUC-3'\n______________UUCUGG___AUGGCUGGCA______GGG\n______________\|:\|\|\|\|___\|::\|\|\|:\|\|\|______\|\|\|\n______________AGGACC___UGUCGAUCGU______CCC\n3'-UUU...CACCA______A____________AAAAUA___AAUAC...UCG-5'\n_____________\|____________________________\|\n_____________41___________________________14\n	86 -- 92	24 -- 30	-24.2509 kcal/mol	8.46179 kcal/mol	4.56973 kcal/mol	73 99@LB@ \| \|@LB@5'-GAC...UCUGC AAC GCA CGAAG...AUC-3'@LB@ UUCUGG AUGGCUGGCA GGG@LB@ \|:\|\|\|\| \|::\|\|\|:\|\|\| \|\|\|@LB@ AGGACC UGUCGAUCGU CCC@LB@3'-UUU...CACCA A AAAAUA AAUAC...UCG-5'@LB@ \| \|@LB@ 41 14@LB@@LB@@LB@Energy -11.22 kcal/mol@LB@Hybridization Energy -24.2509 kcal/mol@LB@Unfolding Energy - mRNA 8.46179 kcal/mol@LB@Unfolding Energy - sRNA 4.56973 kcal/mol@LB@@LB@Position - mRNA 74 -- 98@LB@Position - sRNA 15 -- 40@LB@Position Seed - mRNA 86 -- 92@LB@Position Seed - sRNA 24 -- 30@LB@
44	0.0009392	0.07174	b3453	ugpB	-12.21	0.059079	239 -- 268	1 -- 32	sn-glycerol-3-phosphate ABC transporter periplasmic binding protein	_____________238_______________________________269\n_____________\|_________________________________\|\n5'-UUC...GCGCU___A________A______GA___CACA_____AGUGA...UGG-3'\n______________CGG_CUGGCGUU__AUGGG__AUG______GGC\n______________\|:\|_\|\|:\|\|:\|\|__\|\|\|\|\|__\|\|\|______:\|\|\n______________GUC_GAUCGUAA__UACCC__UAC______UCG\n3'-UUU...ACCAU____________AA_____AA___AAAAAG___-5'\n_____________\|________________________________\|\n_____________33_______________________________1\n	244 -- 250	22 -- 28	-24.6308 kcal/mol	10.9347 kcal/mol	1.49075 kcal/mol	238 269@LB@ \| \|@LB@5'-UUC...GCGCU A A GA CACA AGUGA...UGG-3'@LB@ CGG CUGGCGUU AUGGG AUG GGC@LB@ \|:\| \|\|:\|\|:\|\| \|\|\|\|\| \|\|\| :\|\|@LB@ GUC GAUCGUAA UACCC UAC UCG@LB@3'-UUU...ACCAU AA AA AAAAAG -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -12.21 kcal/mol@LB@Hybridization Energy -24.6308 kcal/mol@LB@Unfolding Energy - mRNA 10.9347 kcal/mol@LB@Unfolding Energy - sRNA 1.49075 kcal/mol@LB@@LB@Position - mRNA 239 -- 268@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 22 -- 28@LB@
128	0.005434	0.142	b1628	rsxB	-10.87	0.114026	241 -- 273	10 -- 44	SoxR iron-sulfur cluster reduction factor component; putative iron-sulfur protein	_____________240___________________________________274\n_____________\|_____________________________________\|\n5'-CAC...CCUGC___G______CGUU____GC_____C___________CCUCC...ACG-3'\n______________UGG__CCUGG____UGGC___CAUU___UGGGUUAUG\n______________\|\|\|__\|\|\|\|\|____::\|\|___\|\|\|\|___\|\|\|\|\|\|\|\|\|\n______________ACC__GGACC____GUCG___GUAA___ACCCAAUAC\n3'-UUU...CCUCC___AA_____AU______AUC____AAU_________AAAAA...UCG-5'\n_____________\|_____________________________________\|\n_____________45____________________________________9\n	267 -- 273	10 -- 16	-28.3112 kcal/mol	12.8396 kcal/mol	4.60525 kcal/mol	240 274@LB@ \| \|@LB@5'-CAC...CCUGC G CGUU GC C CCUCC...ACG-3'@LB@ UGG CCUGG UGGC CAUU UGGGUUAUG@LB@ \|\|\| \|\|\|\|\| ::\|\| \|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ ACC GGACC GUCG GUAA ACCCAAUAC@LB@3'-UUU...CCUCC AA AU AUC AAU AAAAA...UCG-5'@LB@ \| \|@LB@ 45 9@LB@@LB@@LB@Energy -10.87 kcal/mol@LB@Hybridization Energy -28.3112 kcal/mol@LB@Unfolding Energy - mRNA 12.8396 kcal/mol@LB@Unfolding Energy - sRNA 4.60525 kcal/mol@LB@@LB@Position - mRNA 241 -- 273@LB@Position - sRNA 10 -- 44@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 10 -- 16@LB@
176	0.009679	0.1848	b4348	hsdS	-12.85	0.041875	168 -- 192	15 -- 42	specificity determinant for hsdM and hsdR	_____________167__________________________193\n_____________\|____________________________\|\n5'-CUG...CGUCA___G____A____A________G_____GUGAA...UAA-3'\n______________GUU_CUGG___AG__AGCGUUU_GUGGG\n______________\|\|\|_\|\|\|\|___\|\|__\|\|\|:\|\|\|_:\|\|\|\|\n______________CAA_GACC___UC__UCGUAAA_UACCC\n3'-UUU...UCCAC___G____AUG__GA_______A_____AAUAC...UCG-5'\n_____________\|____________________________\|\n_____________43___________________________14\n	180 -- 186	21 -- 27	-24.8178 kcal/mol	7.40251 kcal/mol	4.57031 kcal/mol	167 193@LB@ \| \|@LB@5'-CUG...CGUCA G A A G GUGAA...UAA-3'@LB@ GUU CUGG AG AGCGUUU GUGGG@LB@ \|\|\| \|\|\|\| \|\| \|\|\|:\|\|\| :\|\|\|\|@LB@ CAA GACC UC UCGUAAA UACCC@LB@3'-UUU...UCCAC G AUG GA A AAUAC...UCG-5'@LB@ \| \|@LB@ 43 14@LB@@LB@@LB@Energy -12.85 kcal/mol@LB@Hybridization Energy -24.8178 kcal/mol@LB@Unfolding Energy - mRNA 7.40251 kcal/mol@LB@Unfolding Energy - sRNA 4.57031 kcal/mol@LB@@LB@Position - mRNA 168 -- 192@LB@Position - sRNA 15 -- 42@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 21 -- 27@LB@
9	2.519e-05	0.009407	b0435	bolA	-15.32	0.008970	138 -- 163	15 -- 36	stationary-phase morphogene transcriptional repressor for mreB; also regulator for dacA dacC and ampC	_____________137________________________164\n_____________\|__________________________\|\n5'-UGA...GAAAC___AAAA_____________AAA___AUGGA...CCG-3'\n______________GGU____GCGGCUAGUAUUU___GGG\n______________\|\|\|____:\|:\|\|\|\|\|:\|\|\|\|___\|\|\|\n______________CCA____UGUCGAUCGUAAA___CCC\n3'-UUU...AAGGA____________________AUA___AAUAC...UCG-5'\n_____________\|__________________________\|\n_____________37_________________________14\n	151 -- 157	21 -- 27	-22.9811 kcal/mol	6.21269 kcal/mol	1.45166 kcal/mol	137 164@LB@ \| \|@LB@5'-UGA...GAAAC AAAA AAA AUGGA...CCG-3'@LB@ GGU GCGGCUAGUAUUU GGG@LB@ \|\|\| :\|:\|\|\|\|\|:\|\|\|\| \|\|\|@LB@ CCA UGUCGAUCGUAAA CCC@LB@3'-UUU...AAGGA AUA AAUAC...UCG-5'@LB@ \| \|@LB@ 37 14@LB@@LB@@LB@Energy -15.32 kcal/mol@LB@Hybridization Energy -22.9811 kcal/mol@LB@Unfolding Energy - mRNA 6.21269 kcal/mol@LB@Unfolding Energy - sRNA 1.45166 kcal/mol@LB@@LB@Position - mRNA 138 -- 163@LB@Position - sRNA 15 -- 36@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 21 -- 27@LB@
70	0.00193	0.09081	b1823	cspC	-11.95	0.067388	30 -- 62	1 -- 36	stress protein member of the CspA-family	_____________29___________________________________63\n_____________\|____________________________________\|\n5'-UAU...AACGA____________UG______U__GGCA_________AAAGA...UCU-3'\n______________GGUACAGUU__C__UUUAUG_GU_____UUUUCAGU\n______________\|\|\|\|\|\|\|:\|__\|__\|\|\|\|\|\|_\|\|_____\|\|\|\|\|\|\|:\n______________CCAUGUCGA__G__AAAUAC_CA_____AAAAGUCG\n3'-UUU...AAGGA_________UC_UA______C__AUACA________-5'\n_____________\|___________________________________\|\n_____________37__________________________________1\n	56 -- 62	1 -- 7	-24.9618 kcal/mol	11.5162 kcal/mol	1.49509 kcal/mol	29 63@LB@ \| \|@LB@5'-UAU...AACGA UG U GGCA AAAGA...UCU-3'@LB@ GGUACAGUU C UUUAUG GU UUUUCAGU@LB@ \|\|\|\|\|\|\|:\| \| \|\|\|\|\|\| \|\| \|\|\|\|\|\|\|:@LB@ CCAUGUCGA G AAAUAC CA AAAAGUCG@LB@3'-UUU...AAGGA UC UA C AUACA -5'@LB@ \| \|@LB@ 37 1@LB@@LB@@LB@Energy -11.95 kcal/mol@LB@Hybridization Energy -24.9618 kcal/mol@LB@Unfolding Energy - mRNA 11.5162 kcal/mol@LB@Unfolding Energy - sRNA 1.49509 kcal/mol@LB@@LB@Position - mRNA 30 -- 62@LB@Position - sRNA 1 -- 36@LB@Position Seed - mRNA 56 -- 62@LB@Position Seed - sRNA 1 -- 7@LB@
147	0.006963	0.1592	b0723	sdhA	-11.23	0.096056	156 -- 186	10 -- 46	succinate dehydrogenase flavoprotein subunit	_____________155_______________________________________187\n_____________\|_________________________________________\|\n5'-GGU...GCACU________AC_____________A_______AUUC______GUGUG...GUG-3'\n______________GGUGGUUU____________GUG_UUUAUGG____GUUGUG\n______________\|\|\|\|\|\|\|:____________\|::_\|\|\|\|\|\|\|____\|\|\|:\|\|\n______________CCACCAAG____________CGU_AAAUACC____CAAUAC\n3'-UUU...UUCCU________GACCAUGUCGAU___A_________________AAAAA...UCG-5'\n_____________\|_________________________________________\|\n_____________47________________________________________9\n	170 -- 176	16 -- 22	-22.0315 kcal/mol	6.19365 kcal/mol	4.60552 kcal/mol	155 187@LB@ \| \|@LB@5'-GGU...GCACU AC A AUUC GUGUG...GUG-3'@LB@ GGUGGUUU GUG UUUAUGG GUUGUG@LB@ \|\|\|\|\|\|\|: \|:: \|\|\|\|\|\|\| \|\|\|:\|\|@LB@ CCACCAAG CGU AAAUACC CAAUAC@LB@3'-UUU...UUCCU GACCAUGUCGAU A AAAAA...UCG-5'@LB@ \| \|@LB@ 47 9@LB@@LB@@LB@Energy -11.23 kcal/mol@LB@Hybridization Energy -22.0315 kcal/mol@LB@Unfolding Energy - mRNA 6.19365 kcal/mol@LB@Unfolding Energy - sRNA 4.60552 kcal/mol@LB@@LB@Position - mRNA 156 -- 186@LB@Position - sRNA 10 -- 46@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 16 -- 22@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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