Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
76	0.004413	0.2038	b3211	yhcC	-9.63	0.312909	148 -- 162	49 -- 62	putative Fe-S oxidoreductase Radical SAM superfamily protein	_____________147_____________163\n_____________\|_______________\|\n5'-UGC...CGAAU______AA_______AGGCU...GCC-3'\n______________UGAGCU__AAAUGGC\n______________\|\|\|:\|:__\|\|\|\|\|\|\|\n______________ACUUGG__UUUACCG\n3'-UUU...UUGGA______C________CCCCA...CCG-5'\n_____________\|_______________\|\n_____________63______________48\n	156 -- 162	49 -- 55	-15.5959 kcal/mol	2.00852 kcal/mol	3.95968 kcal/mol	147 163@LB@ \| \|@LB@5'-UGC...CGAAU AA AGGCU...GCC-3'@LB@ UGAGCU AAAUGGC@LB@ \|\|\|:\|: \|\|\|\|\|\|\|@LB@ ACUUGG UUUACCG@LB@3'-UUU...UUGGA C CCCCA...CCG-5'@LB@ \| \|@LB@ 63 48@LB@@LB@@LB@Energy -9.63 kcal/mol@LB@Hybridization Energy -15.5959 kcal/mol@LB@Unfolding Energy - mRNA 2.00852 kcal/mol@LB@Unfolding Energy - sRNA 3.95968 kcal/mol@LB@@LB@Position - mRNA 148 -- 162@LB@Position - sRNA 49 -- 62@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 49 -- 55@LB@
71	0.003993	0.1953	b2347	yfdC	-11.68	0.141997	251 -- 269	1 -- 17	putative inner membrane protein	_____________250__________________270\n_____________\|____________________\|\n5'-GCA...GAGAG_______AAA______C___AAAAA...UCC-3'\n______________CGAAGAA___GAGC_G_GGC\n______________\|:\|\|\|\|\|___:\|\|\|_\|_\|\|\|\n______________GUUUCUU___UUCG_C_CCG\n3'-UUU...CUGUA______________U_A___-5'\n_____________\|___________________\|\n_____________18__________________1\n	251 -- 257	11 -- 17	-16.1242 kcal/mol	3.00377 kcal/mol	1.43853 kcal/mol	250 270@LB@ \| \|@LB@5'-GCA...GAGAG AAA C AAAAA...UCC-3'@LB@ CGAAGAA GAGC G GGC@LB@ \|:\|\|\|\|\| :\|\|\| \| \|\|\|@LB@ GUUUCUU UUCG C CCG@LB@3'-UUU...CUGUA U A -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -11.68 kcal/mol@LB@Hybridization Energy -16.1242 kcal/mol@LB@Unfolding Energy - mRNA 3.00377 kcal/mol@LB@Unfolding Energy - sRNA 1.43853 kcal/mol@LB@@LB@Position - mRNA 251 -- 269@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 251 -- 257@LB@Position Seed - sRNA 11 -- 17@LB@
125	0.009022	0.2491	b0658	ybeX	-16.01	0.015431	14 -- 34	5 -- 21	putative ion transport	_____________13____________________35\n_____________\|_____________________\|\n5'-UUA...CGAUC__________UGAC_______AAGAA...ACC-3'\n______________ACAUCGAAGA____GAAGCAG\n______________\|\|\|\|\|:\|\|\|\|____:\|\|\|\|\|\|\n______________UGUAGUUUCU____UUUCGUC\n3'-UUU...ACCCC_____________________ACCG-5'\n_____________\|_____________________\|\n_____________22____________________4\n	28 -- 34	5 -- 11	-20.2475 kcal/mol	2.73159 kcal/mol	1.5073 kcal/mol	13 35@LB@ \| \|@LB@5'-UUA...CGAUC UGAC AAGAA...ACC-3'@LB@ ACAUCGAAGA GAAGCAG@LB@ \|\|\|\|\|:\|\|\|\| :\|\|\|\|\|\|@LB@ UGUAGUUUCU UUUCGUC@LB@3'-UUU...ACCCC ACCG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -16.01 kcal/mol@LB@Hybridization Energy -20.2475 kcal/mol@LB@Unfolding Energy - mRNA 2.73159 kcal/mol@LB@Unfolding Energy - sRNA 1.5073 kcal/mol@LB@@LB@Position - mRNA 14 -- 34@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 5 -- 11@LB@
193	0.01407	0.2529	b3582	sgbU	-12.18	0.114391	219 -- 241	1 -- 24	putative L-xylulose 5-phosphate 3-epimerase	_____________218______________________242\n_____________\|________________________\|\n5'-UCU...AGUUA_________UGA_______C____GAAAG...UUG-3'\n______________GGGAU_UUA___AAAAGCG_UGGC\n______________\|\|\|\|:_\|:\|___\|\|\|\|\|\|:_\|\|\|\|\n______________CCCUG_AGU___UUUUCGU_ACCG\n3'-UUU...UUUAC_____U___UUC_______C____-5'\n_____________\|_______________________\|\n_____________25______________________1\n	230 -- 236	6 -- 12	-20.9157 kcal/mol	6.29567 kcal/mol	2.44282 kcal/mol	218 242@LB@ \| \|@LB@5'-UCU...AGUUA UGA C GAAAG...UUG-3'@LB@ GGGAU UUA AAAAGCG UGGC@LB@ \|\|\|\|: \|:\| \|\|\|\|\|\|: \|\|\|\|@LB@ CCCUG AGU UUUUCGU ACCG@LB@3'-UUU...UUUAC U UUC C -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -12.18 kcal/mol@LB@Hybridization Energy -20.9157 kcal/mol@LB@Unfolding Energy - mRNA 6.29567 kcal/mol@LB@Unfolding Energy - sRNA 2.44282 kcal/mol@LB@@LB@Position - mRNA 219 -- 241@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 6 -- 12@LB@
59	0.003042	0.1789	b4132	cadB	-12.03	0.121895	256 -- 272	4 -- 32	putative lysine/cadaverine transporter	_____________255___________________________273\n_____________\|_____________________________\|\n5'-UCA...CGGUA___U_________________________AUUGC...CAA-3'\n______________AUA_GAUGGGGA____________GCGGU\n______________\|:\|_:\|\|\|\|\|\|\|____________\|\|:\|\|\n______________UGU_UUACCCCU____________CGUCA\n3'-UUU...CGAGG___U________GUAGUUUCUUUU_____CCG-5'\n_____________\|_____________________________\|\n_____________33____________________________3\n	261 -- 267	21 -- 27	-16.7324 kcal/mol	2.16267 kcal/mol	2.53583 kcal/mol	255 273@LB@ \| \|@LB@5'-UCA...CGGUA U AUUGC...CAA-3'@LB@ AUA GAUGGGGA GCGGU@LB@ \|:\| :\|\|\|\|\|\|\| \|\|:\|\|@LB@ UGU UUACCCCU CGUCA@LB@3'-UUU...CGAGG U GUAGUUUCUUUU CCG-5'@LB@ \| \|@LB@ 33 3@LB@@LB@@LB@Energy -12.03 kcal/mol@LB@Hybridization Energy -16.7324 kcal/mol@LB@Unfolding Energy - mRNA 2.16267 kcal/mol@LB@Unfolding Energy - sRNA 2.53583 kcal/mol@LB@@LB@Position - mRNA 256 -- 272@LB@Position - sRNA 4 -- 32@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 21 -- 27@LB@
180	0.01303	0.2504	b3487	yhiI	-13.61	0.058128	230 -- 256	1 -- 27	putative membrane fusion protein (MFP) of efflux pump	_____________229__________________________257\n_____________\|____________________________\|\n5'-UUU...GCGUG_____U________UUACU_________GGCUA...CGG-3'\n______________GUGGG__UGUCGGG_____GGCGGUGGC\n______________:\|\|\|\|__::\|\|:::_____:\|\|:\|\|\|\|\|\n______________UACCC__GUAGUUU_____UCGUCACCG\n3'-UUU...UGUUU_____CU_______CUUU__________-5'\n_____________\|___________________________\|\n_____________28__________________________1\n	250 -- 256	1 -- 7	-27.1902 kcal/mol	11.0661 kcal/mol	2.51867 kcal/mol	229 257@LB@ \| \|@LB@5'-UUU...GCGUG U UUACU GGCUA...CGG-3'@LB@ GUGGG UGUCGGG GGCGGUGGC@LB@ :\|\|\|\| ::\|\|::: :\|\|:\|\|\|\|\|@LB@ UACCC GUAGUUU UCGUCACCG@LB@3'-UUU...UGUUU CU CUUU -5'@LB@ \| \|@LB@ 28 1@LB@@LB@@LB@Energy -13.61 kcal/mol@LB@Hybridization Energy -27.1902 kcal/mol@LB@Unfolding Energy - mRNA 11.0661 kcal/mol@LB@Unfolding Energy - sRNA 2.51867 kcal/mol@LB@@LB@Position - mRNA 230 -- 256@LB@Position - sRNA 1 -- 27@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 1 -- 7@LB@
120	0.00842	0.2462	b1068	yceM	-12.88	0.082928	190 -- 205	9 -- 24	putative oxidoreductase	_____________189______________206\n_____________\|________________\|\n5'-GCG...CAUCU____G_______U___AAAAU...GAG-3'\n______________GGGA_AUUAAAG_GAA\n______________\|\|\|\|_\|\|:\|\|\|\|_:\|\|\n______________CCCU_UAGUUUC_UUU\n3'-UUU...UUUAC____G_______U___CGUCACCG-5'\n_____________\|________________\|\n_____________25_______________8\n	195 -- 201	13 -- 19	-15.5519 kcal/mol	2.0153 kcal/mol	0.659805 kcal/mol	189 206@LB@ \| \|@LB@5'-GCG...CAUCU G U AAAAU...GAG-3'@LB@ GGGA AUUAAAG GAA@LB@ \|\|\|\| \|\|:\|\|\|\| :\|\|@LB@ CCCU UAGUUUC UUU@LB@3'-UUU...UUUAC G U CGUCACCG-5'@LB@ \| \|@LB@ 25 8@LB@@LB@@LB@Energy -12.88 kcal/mol@LB@Hybridization Energy -15.5519 kcal/mol@LB@Unfolding Energy - mRNA 2.0153 kcal/mol@LB@Unfolding Energy - sRNA 0.659805 kcal/mol@LB@@LB@Position - mRNA 190 -- 205@LB@Position - sRNA 9 -- 24@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 13 -- 19@LB@
90	0.005632	0.2147	b1234	rssA	-9.83	0.291555	191 -- 222	1 -- 26	putative patatin-like family phospholipase	_____________190_______________________________223\n_____________\|_________________________________\|\n5'-GAU...AAUCU__C____AUAAU_______AUAAAAA_______UGGCG...AAA-3'\n______________UG_GGGA_____GAGAAAG_______UAG_GGC\n______________\|\|_\|\|\|\|_____:\|\|\|\|\|:_______:\|\|_\|\|\|\n______________AC_CCCU_____UUCUUUU_______GUC_CCG\n3'-UUU...GUUUU_______GUAGU_______C_________A___-5'\n_____________\|________________________________\|\n_____________27_______________________________1\n	203 -- 209	9 -- 15	-16.1024 kcal/mol	3.75149 kcal/mol	2.51842 kcal/mol	190 223@LB@ \| \|@LB@5'-GAU...AAUCU C AUAAU AUAAAAA UGGCG...AAA-3'@LB@ UG GGGA GAGAAAG UAG GGC@LB@ \|\| \|\|\|\| :\|\|\|\|\|: :\|\| \|\|\|@LB@ AC CCCU UUCUUUU GUC CCG@LB@3'-UUU...GUUUU GUAGU C A -5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -9.83 kcal/mol@LB@Hybridization Energy -16.1024 kcal/mol@LB@Unfolding Energy - mRNA 3.75149 kcal/mol@LB@Unfolding Energy - sRNA 2.51842 kcal/mol@LB@@LB@Position - mRNA 191 -- 222@LB@Position - sRNA 1 -- 26@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 9 -- 15@LB@
57	0.003017	0.1789	b2950	yggR	-13.19	0.071427	205 -- 223	1 -- 21	putative PilT family AAA+ ATPase	_____________204___________________224\n_____________\|_____________________\|\n5'-UUC...UAUGA____G_______UU_______CCUUA...GAA-3'\n______________AUAU_GAAGAAA____GUGGC\n______________\|:\|\|_:\|\|\|\|\|\|____\|\|\|\|\|\n______________UGUA_UUUCUUU____CACCG\n3'-UUU...ACCCC____G_______UCGU_____-5'\n_____________\|____________________\|\n_____________22___________________1\n	210 -- 216	10 -- 16	-17.7325 kcal/mol	3.03326 kcal/mol	1.51103 kcal/mol	204 224@LB@ \| \|@LB@5'-UUC...UAUGA G UU CCUUA...GAA-3'@LB@ AUAU GAAGAAA GUGGC@LB@ \|:\|\| :\|\|\|\|\|\| \|\|\|\|\|@LB@ UGUA UUUCUUU CACCG@LB@3'-UUU...ACCCC G UCGU -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -13.19 kcal/mol@LB@Hybridization Energy -17.7325 kcal/mol@LB@Unfolding Energy - mRNA 3.03326 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 205 -- 223@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 10 -- 16@LB@
89	0.005593	0.2147	b3398	yrfF	-14.72	0.032340	186 -- 206	1 -- 31	putative RcsCDB-response attenuator inner membrane protein	_____________185______________________________207\n_____________\|________________________________\|\n5'-UUA...CUAAG_____________________________A__ACCAU...GGA-3'\n______________UAAGAUGGGGA__________AAGCA_UG_GC\n______________:\|\|:\|\|\|\|\|\|\|__________\|\|\|\|\|_\|\|_\|\|\n______________GUUUUACCCCU__________UUCGU_AC_CG\n3'-UUU...GAGGU___________GUAGUUUCUU_____C_____-5'\n_____________\|_______________________________\|\n_____________32______________________________1\n	190 -- 196	21 -- 27	-21.8606 kcal/mol	4.59782 kcal/mol	2.53929 kcal/mol	185 207@LB@ \| \|@LB@5'-UUA...CUAAG A ACCAU...GGA-3'@LB@ UAAGAUGGGGA AAGCA UG GC@LB@ :\|\|:\|\|\|\|\|\|\| \|\|\|\|\| \|\| \|\|@LB@ GUUUUACCCCU UUCGU AC CG@LB@3'-UUU...GAGGU GUAGUUUCUU C -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -14.72 kcal/mol@LB@Hybridization Energy -21.8606 kcal/mol@LB@Unfolding Energy - mRNA 4.59782 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 186 -- 206@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 21 -- 27@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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