Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
79	0.005218	0.2128	b1264	trpE	-7.84	0.066605	225 -- 250	34 -- 59	component I of anthranilate synthase	_____________224__________________________251\n_____________\|____________________________\|\n5'-UGU...CUCUC_________AACCU______________UCGCG...CGG-3'\n______________GAAC_UGCU_____GCGA_AGGCGCUUA\n______________:\|\|\|_\|\|\|\|_____\|\|:\|_\|:\|\|:\|\|\|\|\n______________UUUG_ACGA_____CGUU_UUCGUGAAU\n3'-UUU...CCUAC____A____AUU______C_________UUUUU...CAA-5'\n_____________\|____________________________\|\n_____________60___________________________33\n	244 -- 250	34 -- 40	-20.2106 kcal/mol	6.10702 kcal/mol	6.26371 kcal/mol	224 251@LB@ \| \|@LB@5'-UGU...CUCUC AACCU UCGCG...CGG-3'@LB@ GAAC UGCU GCGA AGGCGCUUA@LB@ :\|\|\| \|\|\|\| \|\|:\| \|:\|\|:\|\|\|\|@LB@ UUUG ACGA CGUU UUCGUGAAU@LB@3'-UUU...CCUAC A AUU C UUUUU...CAA-5'@LB@ \| \|@LB@ 60 33@LB@@LB@@LB@Energy -7.84 kcal/mol@LB@Hybridization Energy -20.2106 kcal/mol@LB@Unfolding Energy - mRNA 6.10702 kcal/mol@LB@Unfolding Energy - sRNA 6.26371 kcal/mol@LB@@LB@Position - mRNA 225 -- 250@LB@Position - sRNA 34 -- 59@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 34 -- 40@LB@
51	0.002326	0.1469	b2780	pyrG	-6.37	0.158020	19 -- 28	33 -- 42	CTP synthetase	_____________18_________29\n_____________\|__________\|\n5'-UGU...AUGAC__________UUUGC...GCC-3'\n______________AAGCGCUUGA\n______________\|\|\|\|:\|\|\|:\|\n______________UUCGUGAAUU\n3'-UUU...CGUUC__________UUUUA...CAA-5'\n_____________\|__________\|\n_____________43_________32\n	22 -- 28	33 -- 39	-10.9983 kcal/mol	3.00927 kcal/mol	1.61944 kcal/mol	18 29@LB@ \| \|@LB@5'-UGU...AUGAC UUUGC...GCC-3'@LB@ AAGCGCUUGA@LB@ \|\|\|\|:\|\|\|:\|@LB@ UUCGUGAAUU@LB@3'-UUU...CGUUC UUUUA...CAA-5'@LB@ \| \|@LB@ 43 32@LB@@LB@@LB@Energy -6.37 kcal/mol@LB@Hybridization Energy -10.9983 kcal/mol@LB@Unfolding Energy - mRNA 3.00927 kcal/mol@LB@Unfolding Energy - sRNA 1.61944 kcal/mol@LB@@LB@Position - mRNA 19 -- 28@LB@Position - sRNA 33 -- 42@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 33 -- 39@LB@
92	0.006692	0.2343	b2421	cysM	-10.79	0.009324	40 -- 63	37 -- 60	cysteine synthase B (O-acetylserine sulfhydrolase B)	_____________39_______________________64\n_____________\|________________________\|\n5'-GCU...GAUGA__________CUC___CA______CUGAU...GCA-3'\n______________GGAACUUGCU___GCA__AAGCGC\n______________\|:\|\|\|\|\|\|\|\|___\|\|\|__\|\|\|\|:\|\n______________CUUUGAACGA___CGU__UUCGUG\n3'-UUU...CCCUA__________AUU___UC______AAUUU...CAA-5'\n_____________\|________________________\|\n_____________61_______________________36\n	43 -- 49	51 -- 57	-24.0401 kcal/mol	7.00094 kcal/mol	6.24651 kcal/mol	39 64@LB@ \| \|@LB@5'-GCU...GAUGA CUC CA CUGAU...GCA-3'@LB@ GGAACUUGCU GCA AAGCGC@LB@ \|:\|\|\|\|\|\|\|\| \|\|\| \|\|\|\|:\|@LB@ CUUUGAACGA CGU UUCGUG@LB@3'-UUU...CCCUA AUU UC AAUUU...CAA-5'@LB@ \| \|@LB@ 61 36@LB@@LB@@LB@Energy -10.79 kcal/mol@LB@Hybridization Energy -24.0401 kcal/mol@LB@Unfolding Energy - mRNA 7.00094 kcal/mol@LB@Unfolding Energy - sRNA 6.24651 kcal/mol@LB@@LB@Position - mRNA 40 -- 63@LB@Position - sRNA 37 -- 60@LB@Position Seed - mRNA 43 -- 49@LB@Position Seed - sRNA 51 -- 57@LB@
172	0.01959	0.3668	b0336	codB	-6.02	0.190787	88 -- 108	28 -- 40	cytosine transporter	_____________87____________________109\n_____________\|_____________________\|\n5'-CCA...UUUUU_____CAUUCAUA________AUAUU...UUU-3'\n______________GCACU________UAAAAAAU\n______________\|\|\|\|\|________\|\|\|\|\|\|\|\|\n______________CGUGA________AUUUUUUA\n3'-UUU...UUCUU_____________________AGCAA...CAA-5'\n_____________\|_____________________\|\n_____________41____________________27\n	102 -- 108	28 -- 34	-8.50412 kcal/mol	0.843154 kcal/mol	1.63611 kcal/mol	87 109@LB@ \| \|@LB@5'-CCA...UUUUU CAUUCAUA AUAUU...UUU-3'@LB@ GCACU UAAAAAAU@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ CGUGA AUUUUUUA@LB@3'-UUU...UUCUU AGCAA...CAA-5'@LB@ \| \|@LB@ 41 27@LB@@LB@@LB@Energy -6.02 kcal/mol@LB@Hybridization Energy -8.50412 kcal/mol@LB@Unfolding Energy - mRNA 0.843154 kcal/mol@LB@Unfolding Energy - sRNA 1.63611 kcal/mol@LB@@LB@Position - mRNA 88 -- 108@LB@Position - sRNA 28 -- 40@LB@Position Seed - mRNA 102 -- 108@LB@Position Seed - sRNA 28 -- 34@LB@
54	0.002706	0.1597	b0200	gmhB	-8.11	0.056337	123 -- 141	35 -- 53	D D-heptose 1 7-bisphosphate phosphatase	_____________122_________________142\n_____________\|___________________\|\n5'-AAA...AUCAG_____U____A________UCUUG...ACG-3'\n______________GUUUA_GCGA_GAGCACUU\n______________\|:\|\|\|_\|\|:\|_:\|\|\|\|\|\|\|\n______________CGAAU_CGUU_UUCGUGAA\n3'-UUU...UUGAA_____U____C________UUUUU...CAA-5'\n_____________\|___________________\|\n_____________54__________________34\n	135 -- 141	35 -- 41	-19.8402 kcal/mol	5.62708 kcal/mol	6.10399 kcal/mol	122 142@LB@ \| \|@LB@5'-AAA...AUCAG U A UCUUG...ACG-3'@LB@ GUUUA GCGA GAGCACUU@LB@ \|:\|\|\| \|\|:\| :\|\|\|\|\|\|\|@LB@ CGAAU CGUU UUCGUGAA@LB@3'-UUU...UUGAA U C UUUUU...CAA-5'@LB@ \| \|@LB@ 54 34@LB@@LB@@LB@Energy -8.11 kcal/mol@LB@Hybridization Energy -19.8402 kcal/mol@LB@Unfolding Energy - mRNA 5.62708 kcal/mol@LB@Unfolding Energy - sRNA 6.10399 kcal/mol@LB@@LB@Position - mRNA 123 -- 141@LB@Position - sRNA 35 -- 53@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 35 -- 41@LB@
110	0.009505	0.2693	b0632	dacA	-12.82	0.002052	146 -- 175	26 -- 57	D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5)	_____________145______________________________176\n_____________\|________________________________\|\n5'-CCU...AGUGC_______AU______________UUUU_____CAUCA...AUA-3'\n______________AUUUGCU__AGUAGG__GCACUU____AAUUC\n______________\|:\|\|\|\|\|__\|\|:\|:\|__\|\|\|\|\|\|____\|\|\|\|\|\n______________UGAACGA__UCGUUC__CGUGAA____UUAAG\n3'-UUU...UACUU_______AU______UU______UUUU_____CAAUG...CAA-5'\n_____________\|________________________________\|\n_____________58_______________________________25\n	146 -- 152	51 -- 57	-23.8315 kcal/mol	4.73353 kcal/mol	6.27605 kcal/mol	145 176@LB@ \| \|@LB@5'-CCU...AGUGC AU UUUU CAUCA...AUA-3'@LB@ AUUUGCU AGUAGG GCACUU AAUUC@LB@ \|:\|\|\|\|\| \|\|:\|:\| \|\|\|\|\|\| \|\|\|\|\|@LB@ UGAACGA UCGUUC CGUGAA UUAAG@LB@3'-UUU...UACUU AU UU UUUU CAAUG...CAA-5'@LB@ \| \|@LB@ 58 25@LB@@LB@@LB@Energy -12.82 kcal/mol@LB@Hybridization Energy -23.8315 kcal/mol@LB@Unfolding Energy - mRNA 4.73353 kcal/mol@LB@Unfolding Energy - sRNA 6.27605 kcal/mol@LB@@LB@Position - mRNA 146 -- 175@LB@Position - sRNA 26 -- 57@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 51 -- 57@LB@
116	0.009699	0.2693	b2708	srlQ	-8.08	0.057211	196 -- 214	36 -- 49	D-arabinose 5-phosphate isomerase	_____________195_________________215\n_____________\|___________________\|\n5'-UAC...GGAGA______UGAGU________ACUGA...GCG-3'\n______________GAGCAA_____GAAGCACU\n______________:\|\|\|\|\|_____\|\|\|\|\|\|\|\|\n______________UUCGUU_____CUUCGUGA\n3'-UUU...ACGAA___________________AUUUU...CAA-5'\n_____________\|___________________\|\n_____________50__________________35\n	208 -- 214	36 -- 42	-17.2491 kcal/mol	3.12814 kcal/mol	6.03645 kcal/mol	195 215@LB@ \| \|@LB@5'-UAC...GGAGA UGAGU ACUGA...GCG-3'@LB@ GAGCAA GAAGCACU@LB@ :\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ UUCGUU CUUCGUGA@LB@3'-UUU...ACGAA AUUUU...CAA-5'@LB@ \| \|@LB@ 50 35@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -17.2491 kcal/mol@LB@Unfolding Energy - mRNA 3.12814 kcal/mol@LB@Unfolding Energy - sRNA 6.03645 kcal/mol@LB@@LB@Position - mRNA 196 -- 214@LB@Position - sRNA 36 -- 49@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 36 -- 42@LB@
71	0.00365	0.1656	b4478	dgoD	-6.42	0.153775	171 -- 195	38 -- 57	D-galactonate dehydratase	_____________170_______________________196\n_____________\|_________________________\|\n5'-AAA...GCAGC_______A____GUAUC________GUGCA...UGA-3'\n______________AUUUGUU_AGGC_____GAGAGGCA\n______________\|:\|\|\|:\|_\|:\|\|_____:\|\|\|:\|\|\|\n______________UGAACGA_UUCG_____UUCUUCGU\n3'-UUU...UACUU_______A_________________GAAUU...CAA-5'\n_____________\|_________________________\|\n_____________58________________________37\n	189 -- 195	38 -- 44	-17.6382 kcal/mol	5.02573 kcal/mol	6.19395 kcal/mol	170 196@LB@ \| \|@LB@5'-AAA...GCAGC A GUAUC GUGCA...UGA-3'@LB@ AUUUGUU AGGC GAGAGGCA@LB@ \|:\|\|\|:\| \|:\|\| :\|\|\|:\|\|\|@LB@ UGAACGA UUCG UUCUUCGU@LB@3'-UUU...UACUU A GAAUU...CAA-5'@LB@ \| \|@LB@ 58 37@LB@@LB@@LB@Energy -6.42 kcal/mol@LB@Hybridization Energy -17.6382 kcal/mol@LB@Unfolding Energy - mRNA 5.02573 kcal/mol@LB@Unfolding Energy - sRNA 6.19395 kcal/mol@LB@@LB@Position - mRNA 171 -- 195@LB@Position - sRNA 38 -- 57@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 38 -- 44@LB@
3	4.385e-06	0.004708	b3749	rbsA	-11.98	0.003917	29 -- 86	17 -- 57	D-ribose ABC transporter ATPase	_____________28_________________________________________________________87\n_____________\|__________________________________________________________\|\n5'-UAA...UGCUC___CAC________GCUGCAAAAACACCAG____A___CAUU________________CGCAU...UGG-3'\n______________ACU___CUUGAGCA________________GGAA_UAC____GAAAUUCGUUACACCA\n______________\|\|\|___\|\|\|:\|\|\|\|________________:\|\|\|_:\|\|____:\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________UGA___GAAUUCGU________________UCUU_GUG____UUUUAAGCAAUGUGGU\n3'-UUU...UACUU___AC_____________________________C___AAUU________________CCUUU...CAA-5'\n_____________\|__________________________________________________________\|\n_____________58_________________________________________________________16\n	80 -- 86	17 -- 23	-33.7219 kcal/mol	7.92362 kcal/mol	13.8209 kcal/mol	28 87@LB@ \| \|@LB@5'-UAA...UGCUC CAC GCUGCAAAAACACCAG A CAUU CGCAU...UGG-3'@LB@ ACU CUUGAGCA GGAA UAC GAAAUUCGUUACACCA@LB@ \|\|\| \|\|\|:\|\|\|\| :\|\|\| :\|\| :\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ UGA GAAUUCGU UCUU GUG UUUUAAGCAAUGUGGU@LB@3'-UUU...UACUU AC C AAUU CCUUU...CAA-5'@LB@ \| \|@LB@ 58 16@LB@@LB@@LB@Energy -11.98 kcal/mol@LB@Hybridization Energy -33.7219 kcal/mol@LB@Unfolding Energy - mRNA 7.92362 kcal/mol@LB@Unfolding Energy - sRNA 13.8209 kcal/mol@LB@@LB@Position - mRNA 29 -- 86@LB@Position - sRNA 17 -- 57@LB@Position Seed - mRNA 80 -- 86@LB@Position Seed - sRNA 17 -- 23@LB@
98	0.007325	0.239	b4171	miaA	-8.40	0.046782	42 -- 58	5 -- 24	delta(2)-isopentenylpyrophosphate tRNA-adenosine transferase	_____________41___________________59\n_____________\|____________________\|\n5'-GAA...GUGGA____________________AGCGA...UUU-3'\n______________UUGCAC___GAAAUCUGAUG\n______________\|\|:\|\|\|___\|\|\|\|\|\|\|\|\|\|\|\n______________AAUGUG___CUUUAGACUAC\n3'-UUU...UAAGC______GUC___________ACAA-5'\n_____________\|____________________\|\n_____________25___________________4\n	52 -- 58	5 -- 11	-19.996 kcal/mol	4.00751 kcal/mol	7.58501 kcal/mol	41 59@LB@ \| \|@LB@5'-GAA...GUGGA AGCGA...UUU-3'@LB@ UUGCAC GAAAUCUGAUG@LB@ \|\|:\|\|\| \|\|\|\|\|\|\|\|\|\|\|@LB@ AAUGUG CUUUAGACUAC@LB@3'-UUU...UAAGC GUC ACAA-5'@LB@ \| \|@LB@ 25 4@LB@@LB@@LB@Energy -8.40 kcal/mol@LB@Hybridization Energy -19.996 kcal/mol@LB@Unfolding Energy - mRNA 4.00751 kcal/mol@LB@Unfolding Energy - sRNA 7.58501 kcal/mol@LB@@LB@Position - mRNA 42 -- 58@LB@Position - sRNA 5 -- 24@LB@Position Seed - mRNA 52 -- 58@LB@Position Seed - sRNA 5 -- 11@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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