Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
151	0.006118	0.1406	b1103	hinT	-6.52	0.328434	216 -- 241	45 -- 70	purine nucleoside phosphoramidase dadA activator protein		_____________215________________________242\n_____________\|__________________________\|\n5'-CAA...AAACU_________A_____AUUCGU_____GAUCC...CGC-3'\n______________AUAUUCAGC_AAAUU______CGUGA\n______________\|\|\|\|\|\|\|\|\|_\|\|\|\|:______\|\|\|\|\|\n______________UAUAAGUCG_UUUAG______GCACU\n3'-AUU...GAUUU_________G_____GCUAAU_____UCAUU...AUG-5'\n_____________\|__________________________\|\n_____________71_________________________44\n	218 -- 224	62 -- 68	-20.3535 kcal/mol	5.67357 kcal/mol	8.1779 kcal/mol	215 242@LB@ \| \|@LB@5'-CAA...AAACU A AUUCGU GAUCC...CGC-3'@LB@ AUAUUCAGC AAAUU CGUGA@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|: \|\|\|\|\|@LB@ UAUAAGUCG UUUAG GCACU@LB@3'-AUU...GAUUU G GCUAAU UCAUU...AUG-5'@LB@ \| \|@LB@ 71 44@LB@@LB@@LB@Energy -6.52 kcal/mol@LB@Hybridization Energy -20.3535 kcal/mol@LB@Unfolding Energy - mRNA 5.67357 kcal/mol@LB@Unfolding Energy - sRNA 8.1779 kcal/mol@LB@@LB@Position - mRNA 216 -- 241@LB@Position - sRNA 45 -- 70@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 62 -- 68@LB@
152	0.006159	0.1406	b2467	nudK	-9.74	0.053801	255 -- 261	1 -- 7	GDP-mannose pyrophosphatase		_____________254_____262\n_____________\|_______\|\n5'-CAA...AUUUC_______ACAAC...AAG-3'\n______________ACCCUGC\n______________\|\|\|\|\|:\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	255 -- 261	1 -- 7	-11.9691 kcal/mol	0.21022 kcal/mol	2.03949 kcal/mol	254 262@LB@ \| \|@LB@5'-CAA...AUUUC ACAAC...AAG-3'@LB@ ACCCUGC@LB@ \|\|\|\|\|:\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -11.9691 kcal/mol@LB@Unfolding Energy - mRNA 0.21022 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 255 -- 261@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 1 -- 7@LB@
153	0.006198	0.1406	b3459	panM	-8.50	0.116540	144 -- 151	50 -- 57	PanD autocleavage accelerator panothenate synthesis		_____________143______152\n_____________\|________\|\n5'-AAA...AAGCC________AAUUA...UUG-3'\n______________UCCGAUUA\n______________\|\|\|\|\|\|\|\|\n______________AGGCUAAU\n3'-AUU...GGUUU________GCACU...AUG-5'\n_____________\|________\|\n_____________58_______49\n	145 -- 151	50 -- 56	-10.246 kcal/mol	1.44461 kcal/mol	0.317388 kcal/mol	143 152@LB@ \| \|@LB@5'-AAA...AAGCC AAUUA...UUG-3'@LB@ UCCGAUUA@LB@ \|\|\|\|\|\|\|\|@LB@ AGGCUAAU@LB@3'-AUU...GGUUU GCACU...AUG-5'@LB@ \| \|@LB@ 58 49@LB@@LB@@LB@Energy -8.50 kcal/mol@LB@Hybridization Energy -10.246 kcal/mol@LB@Unfolding Energy - mRNA 1.44461 kcal/mol@LB@Unfolding Energy - sRNA 0.317388 kcal/mol@LB@@LB@Position - mRNA 144 -- 151@LB@Position - sRNA 50 -- 57@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 50 -- 56@LB@
154	0.006224	0.1406	b0882	clpA	-11.36	0.017252	127 -- 158	2 -- 32	ATPase and specificity subunit of ClpA-ClpP ATP-dependent serine protease chaperone activity		_____________126______________________________159\n_____________\|________________________________\|\n5'-UUU...CGCGA______AU_______CAUUG__G_____G___GAAAA...CGC-3'\n______________GGGAGA__GAGCAUC_____CU_UGUAC_CUA\n______________\|::\|\|\|__\|\|:\|\|\|\|_____\|\|_\|\|\|\|\|_\|\|\|\n______________CUUUCU__CUUGUAG_____GA_ACAUG_GAU\n3'-AUU...CCAGA______AU_______AAUG___G_____G___G-5'\n_____________\|________________________________\|\n_____________33_______________________________1\n	135 -- 141	18 -- 24	-27.9684 kcal/mol	7.80814 kcal/mol	8.82442 kcal/mol	126 159@LB@ \| \|@LB@5'-UUU...CGCGA AU CAUUG G G GAAAA...CGC-3'@LB@ GGGAGA GAGCAUC CU UGUAC CUA@LB@ \|::\|\|\| \|\|:\|\|\|\| \|\| \|\|\|\|\| \|\|\|@LB@ CUUUCU CUUGUAG GA ACAUG GAU@LB@3'-AUU...CCAGA AU AAUG G G G-5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -11.36 kcal/mol@LB@Hybridization Energy -27.9684 kcal/mol@LB@Unfolding Energy - mRNA 7.80814 kcal/mol@LB@Unfolding Energy - sRNA 8.82442 kcal/mol@LB@@LB@Position - mRNA 127 -- 158@LB@Position - sRNA 2 -- 32@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 18 -- 24@LB@
155	0.00623	0.1406	b4178	nsrR	-8.53	0.114937	220 -- 228	48 -- 56	nitric oxide-sensitive repressor for NO regulon		_____________219_______229\n_____________\|_________\|\n5'-GGU...UUUCA_________GAUUA...ACG-3'\n______________CUGAUUACG\n______________\|:\|\|\|\|\|\|\|\n______________GGCUAAUGC\n3'-AUU...GUUUA_________ACUUC...AUG-5'\n_____________\|_________\|\n_____________57________47\n	222 -- 228	48 -- 54	-11.8869 kcal/mol	1.78283 kcal/mol	1.55919 kcal/mol	219 229@LB@ \| \|@LB@5'-GGU...UUUCA GAUUA...ACG-3'@LB@ CUGAUUACG@LB@ \|:\|\|\|\|\|\|\|@LB@ GGCUAAUGC@LB@3'-AUU...GUUUA ACUUC...AUG-5'@LB@ \| \|@LB@ 57 47@LB@@LB@@LB@Energy -8.53 kcal/mol@LB@Hybridization Energy -11.8869 kcal/mol@LB@Unfolding Energy - mRNA 1.78283 kcal/mol@LB@Unfolding Energy - sRNA 1.55919 kcal/mol@LB@@LB@Position - mRNA 220 -- 228@LB@Position - sRNA 48 -- 56@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 48 -- 54@LB@
156	0.006236	0.1406	b2922	yggE	-5.46	0.507768	199 -- 207	42 -- 50	oxidative stress defense protein		_____________198_______208\n_____________\|_________\|\n5'-GCA...GACUA_________UCAAA...CCG-3'\n______________ACGUGAAGU\n______________\|\|\|\|\|\|\|\|\|\n______________UGCACUUCA\n3'-AUU...GCUAA_________UUUUC...AUG-5'\n_____________\|_________\|\n_____________51________41\n	201 -- 207	42 -- 48	-12.7727 kcal/mol	4.07491 kcal/mol	3.2504 kcal/mol	198 208@LB@ \| \|@LB@5'-GCA...GACUA UCAAA...CCG-3'@LB@ ACGUGAAGU@LB@ \|\|\|\|\|\|\|\|\|@LB@ UGCACUUCA@LB@3'-AUU...GCUAA UUUUC...AUG-5'@LB@ \| \|@LB@ 51 41@LB@@LB@@LB@Energy -5.46 kcal/mol@LB@Hybridization Energy -12.7727 kcal/mol@LB@Unfolding Energy - mRNA 4.07491 kcal/mol@LB@Unfolding Energy - sRNA 3.2504 kcal/mol@LB@@LB@Position - mRNA 199 -- 207@LB@Position - sRNA 42 -- 50@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 42 -- 48@LB@
157	0.006279	0.1407	b0312	betB	-8.02	0.153308	1 -- 12	52 -- 63	betaine aldehyde dehydrogenase NAD-dependent		______________1___________13\n______________\|___________\|\n___________5'-____________GAGCG...ACG-3'\n______________GUCGAAUCUGGU\n______________\|:\|:\|\|\|\|:\|:\|\n______________CGGUUUAGGCUA\n3'-AUU...UAAGU____________AUGCA...AUG-5'\n_____________\|____________\|\n_____________64___________51\n	6 -- 12	52 -- 58	-15.0997 kcal/mol	0.969406 kcal/mol	6.13017 kcal/mol	1 13@LB@ \| \|@LB@ 5'- GAGCG...ACG-3'@LB@ GUCGAAUCUGGU@LB@ \|:\|:\|\|\|\|:\|:\|@LB@ CGGUUUAGGCUA@LB@3'-AUU...UAAGU AUGCA...AUG-5'@LB@ \| \|@LB@ 64 51@LB@@LB@@LB@Energy -8.02 kcal/mol@LB@Hybridization Energy -15.0997 kcal/mol@LB@Unfolding Energy - mRNA 0.969406 kcal/mol@LB@Unfolding Energy - sRNA 6.13017 kcal/mol@LB@@LB@Position - mRNA 1 -- 12@LB@Position - sRNA 52 -- 63@LB@Position Seed - mRNA 6 -- 12@LB@Position Seed - sRNA 52 -- 58@LB@
158	0.00634	0.1412	b3598	yibI	-10.19	0.039756	289 -- 298	49 -- 58	DUF3302 family inner membrane protein	b3587	_____________288________299\n_____________\|__________\|\n5'-CGU...CCCUU__________CA-3'\n______________AUCUGAUUGC\n______________\|\|\|:\|\|\|\|:\|\n______________UAGGCUAAUG\n3'-AUU...CGGUU__________CACUU...AUG-5'\n_____________\|__________\|\n_____________59_________48\n	292 -- 298	49 -- 55	-10.9433 kcal/mol	0.440755 kcal/mol	0.318367 kcal/mol	288 299@LB@ \| \|@LB@5'-CGU...CCCUU CA-3'@LB@ AUCUGAUUGC@LB@ \|\|\|:\|\|\|\|:\|@LB@ UAGGCUAAUG@LB@3'-AUU...CGGUU CACUU...AUG-5'@LB@ \| \|@LB@ 59 48@LB@@LB@@LB@Energy -10.19 kcal/mol@LB@Hybridization Energy -10.9433 kcal/mol@LB@Unfolding Energy - mRNA 0.440755 kcal/mol@LB@Unfolding Energy - sRNA 0.318367 kcal/mol@LB@@LB@Position - mRNA 289 -- 298@LB@Position - sRNA 49 -- 58@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 49 -- 55@LB@
159	0.006413	0.1413	b4242	mgtA	-7.15	0.243258	247 -- 262	45 -- 58	magnesium transporter		_____________246______________263\n_____________\|________________\|\n5'-GGU...UUCCC________CAU_____UCCAU...UGG-3'\n______________GUCUGGUU___CGUGA\n______________:\|\|:\|:\|\|___\|\|\|\|\|\n______________UAGGCUAA___GCACU\n3'-AUU...CGGUU________U_______UCAUU...AUG-5'\n_____________\|________________\|\n_____________59_______________44\n	248 -- 254	51 -- 57	-12.639 kcal/mol	3.2244 kcal/mol	2.28003 kcal/mol	246 263@LB@ \| \|@LB@5'-GGU...UUCCC CAU UCCAU...UGG-3'@LB@ GUCUGGUU CGUGA@LB@ :\|\|:\|:\|\| \|\|\|\|\|@LB@ UAGGCUAA GCACU@LB@3'-AUU...CGGUU U UCAUU...AUG-5'@LB@ \| \|@LB@ 59 44@LB@@LB@@LB@Energy -7.15 kcal/mol@LB@Hybridization Energy -12.639 kcal/mol@LB@Unfolding Energy - mRNA 3.2244 kcal/mol@LB@Unfolding Energy - sRNA 2.28003 kcal/mol@LB@@LB@Position - mRNA 247 -- 262@LB@Position - sRNA 45 -- 58@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 51 -- 57@LB@
160	0.006479	0.1413	b0391	yaiE	-12.00	0.010520	148 -- 162	1 -- 15	UPF0345 family protein		_____________147_____________163\n_____________\|_______________\|\n5'-GAU...CCAGC_______GC______AGUGA...GCG-3'\n______________GCCUCUG__CCCUAU\n______________:\|\|\|\|\|\|__\|\|\|\|\|:\n______________UGGAGAC__GGGAUG\n3'-AUU...UAGAA_______AU______-5'\n_____________\|______________\|\n_____________16_____________1\n	148 -- 154	9 -- 15	-21.6181 kcal/mol	3.81195 kcal/mol	5.82808 kcal/mol	147 163@LB@ \| \|@LB@5'-GAU...CCAGC GC AGUGA...GCG-3'@LB@ GCCUCUG CCCUAU@LB@ :\|\|\|\|\|\| \|\|\|\|\|:@LB@ UGGAGAC GGGAUG@LB@3'-AUU...UAGAA AU -5'@LB@ \| \|@LB@ 16 1@LB@@LB@@LB@Energy -12.00 kcal/mol@LB@Hybridization Energy -21.6181 kcal/mol@LB@Unfolding Energy - mRNA 3.81195 kcal/mol@LB@Unfolding Energy - sRNA 5.82808 kcal/mol@LB@@LB@Position - mRNA 148 -- 162@LB@Position - sRNA 1 -- 15@LB@Position Seed - mRNA 148 -- 154@LB@Position Seed - sRNA 9 -- 15@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)

Job resubmission

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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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