Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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
137	0.02312	0.5385	b2153	folE	-12.97	0.031813	230 -- 265	52 -- 87	GTP cyclohydrolase I	_____________229___________________________________266\n_____________\|_____________________________________\|\n5'-CUG...GCCCU________AA___G_______CG____GACU______ACCGC...ACG-3'\n______________GGUUCAUG___GC_UUAGUUG__CGAG____GGAAAC\n______________:\|\|\|\|\|:\|___\|\|_\|\|\|\|\|\|:__\|\|\|\|____:\|\|\|\|\|\n______________UCAAGUGC___CG_AAUCAAU__GCUC____UCUUUG\n3'-CGC...CGUUU________AAC__A_______AA____AAC_______AGAGC...AAG-5'\n_____________\|_____________________________________\|\n_____________88____________________________________51\n	243 -- 249	67 -- 73	-29.7116 kcal/mol	12.3362 kcal/mol	4.40736 kcal/mol	229 266@LB@ \| \|@LB@5'-CUG...GCCCU AA G CG GACU ACCGC...ACG-3'@LB@ GGUUCAUG GC UUAGUUG CGAG GGAAAC@LB@ :\|\|\|\|\|:\| \|\| \|\|\|\|\|\|: \|\|\|\| :\|\|\|\|\|@LB@ UCAAGUGC CG AAUCAAU GCUC UCUUUG@LB@3'-CGC...CGUUU AAC A AA AAC AGAGC...AAG-5'@LB@ \| \|@LB@ 88 51@LB@@LB@@LB@Energy -12.97 kcal/mol@LB@Hybridization Energy -29.7116 kcal/mol@LB@Unfolding Energy - mRNA 12.3362 kcal/mol@LB@Unfolding Energy - sRNA 4.40736 kcal/mol@LB@@LB@Position - mRNA 230 -- 265@LB@Position - sRNA 52 -- 87@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 67 -- 73@LB@
93	0.01594	0.5385	b3430	glgC	-8.76	0.171477	231 -- 238	75 -- 82	glucose-1-phosphate adenylyltransferase	_____________230______239\n_____________\|________\|\n5'-CAG...ACUUA________GCGCC...UGA-3'\n______________AUGUUGGC\n______________\|:\|\|\|\|\|\|\n______________UGCAACCG\n3'-CGC...UCAAG________AAAUC...AAG-5'\n_____________\|________\|\n_____________83_______74\n	232 -- 238	75 -- 81	-11.9398 kcal/mol	2.84031 kcal/mol	0.339284 kcal/mol	230 239@LB@ \| \|@LB@5'-CAG...ACUUA GCGCC...UGA-3'@LB@ AUGUUGGC@LB@ \|:\|\|\|\|\|\|@LB@ UGCAACCG@LB@3'-CGC...UCAAG AAAUC...AAG-5'@LB@ \| \|@LB@ 83 74@LB@@LB@@LB@Energy -8.76 kcal/mol@LB@Hybridization Energy -11.9398 kcal/mol@LB@Unfolding Energy - mRNA 2.84031 kcal/mol@LB@Unfolding Energy - sRNA 0.339284 kcal/mol@LB@@LB@Position - mRNA 231 -- 238@LB@Position - sRNA 75 -- 82@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 75 -- 81@LB@
5	0.0009313	0.5385	b3829	metE	-12.51	0.038445	233 -- 242	75 -- 84	5-methyltetrahydropteroyltriglutamate- homocysteine S-methyltransferase	_____________232________243\n_____________\|__________\|\n5'-GAG...UUCCC__________CUGCG...GUG-3'\n______________UCGCGUUGGC\n______________\|\|:\|\|\|\|\|\|\|\n______________AGUGCAACCG\n3'-CGC...UUUCA__________AAAUC...AAG-5'\n_____________\|__________\|\n_____________85_________74\n	236 -- 242	75 -- 81	-17.7887 kcal/mol	4.77726 kcal/mol	0.505918 kcal/mol	232 243@LB@ \| \|@LB@5'-GAG...UUCCC CUGCG...GUG-3'@LB@ UCGCGUUGGC@LB@ \|\|:\|\|\|\|\|\|\|@LB@ AGUGCAACCG@LB@3'-CGC...UUUCA AAAUC...AAG-5'@LB@ \| \|@LB@ 85 74@LB@@LB@@LB@Energy -12.51 kcal/mol@LB@Hybridization Energy -17.7887 kcal/mol@LB@Unfolding Energy - mRNA 4.77726 kcal/mol@LB@Unfolding Energy - sRNA 0.505918 kcal/mol@LB@@LB@Position - mRNA 233 -- 242@LB@Position - sRNA 75 -- 84@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 75 -- 81@LB@
85	0.01519	0.5385	b0094	ftsA	-12.00	0.047343	234 -- 271	69 -- 107	ATP-binding cell division FtsK recruitment protein	_____________233__________________________________________272\n_____________\|____________________________________________\|\n5'-AAU...UAGUA_____________UGGUA___________GC_____________AGGGG...UCA-3'\n______________GGA__CUGGAGAU_____CCGCGAAGGUU__C____GCUUUAGU\n______________\|\|\|__\|\|\|\|\|\|\|\|_____\|\|\|\|:\|\|:\|\|\|__\|____\|\|\|\|\|\|\|\|\n______________CCU__GACCUCUA_____GGCGUUUUCAA__G____CGAAAUCA\n_________3'-CG___AG________________________GU_CAAC________AUAAG...AAG-5'\n_____________\|____________________________________________\|\n_____________108__________________________________________68\n	265 -- 271	69 -- 75	-38.6824 kcal/mol	14.7528 kcal/mol	11.9342 kcal/mol	233 272@LB@ \| \|@LB@5'-AAU...UAGUA UGGUA GC AGGGG...UCA-3'@LB@ GGA CUGGAGAU CCGCGAAGGUU C GCUUUAGU@LB@ \|\|\| \|\|\|\|\|\|\|\| \|\|\|\|:\|\|:\|\|\| \| \|\|\|\|\|\|\|\|@LB@ CCU GACCUCUA GGCGUUUUCAA G CGAAAUCA@LB@ 3'-CG AG GU CAAC AUAAG...AAG-5'@LB@ \| \|@LB@ 108 68@LB@@LB@@LB@Energy -12.00 kcal/mol@LB@Hybridization Energy -38.6824 kcal/mol@LB@Unfolding Energy - mRNA 14.7528 kcal/mol@LB@Unfolding Energy - sRNA 11.9342 kcal/mol@LB@@LB@Position - mRNA 234 -- 271@LB@Position - sRNA 69 -- 107@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 69 -- 75@LB@
89	0.01549	0.5385	b3147	lpoA	-11.44	0.059349	235 -- 255	64 -- 83	OM lipoprotein stimulator of MrcA transpeptidase	_____________234___________________256\n_____________\|_____________________\|\n5'-UAU...AGCCG_______U__GCCU_______UGGCA...AUC-3'\n______________CGCGUUG_CU____GUUGUUC\n______________\|:\|\|\|\|\|_\|\|____\|\|\|:\|\|\|\n______________GUGCAAC_GA____CAAUAAG\n3'-CGC...UUCAA_______C__AAU________CUCAA...AAG-5'\n_____________\|_____________________\|\n_____________84____________________63\n	249 -- 255	64 -- 70	-16.9353 kcal/mol	4.93537 kcal/mol	0.560651 kcal/mol	234 256@LB@ \| \|@LB@5'-UAU...AGCCG U GCCU UGGCA...AUC-3'@LB@ CGCGUUG CU GUUGUUC@LB@ \|:\|\|\|\|\| \|\| \|\|\|:\|\|\|@LB@ GUGCAAC GA CAAUAAG@LB@3'-CGC...UUCAA C AAU CUCAA...AAG-5'@LB@ \| \|@LB@ 84 63@LB@@LB@@LB@Energy -11.44 kcal/mol@LB@Hybridization Energy -16.9353 kcal/mol@LB@Unfolding Energy - mRNA 4.93537 kcal/mol@LB@Unfolding Energy - sRNA 0.560651 kcal/mol@LB@@LB@Position - mRNA 235 -- 255@LB@Position - sRNA 64 -- 83@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 64 -- 70@LB@
148	0.0249	0.5467	b2131	osmF	-10.26	0.095288	236 -- 244	75 -- 83	putative ABC transporter periplasmic binding protein	_____________235_______245\n_____________\|_________\|\n5'-AGG...CUGGU_________AGCCG...UCG-3'\n______________UAUGUUGGC\n______________:\|:\|\|\|\|\|\|\n______________GUGCAACCG\n3'-CGC...UUCAA_________AAAUC...AAG-5'\n_____________\|_________\|\n_____________84________74\n	238 -- 244	75 -- 81	-12.6611 kcal/mol	1.90691 kcal/mol	0.492259 kcal/mol	235 245@LB@ \| \|@LB@5'-AGG...CUGGU AGCCG...UCG-3'@LB@ UAUGUUGGC@LB@ :\|:\|\|\|\|\|\|@LB@ GUGCAACCG@LB@3'-CGC...UUCAA AAAUC...AAG-5'@LB@ \| \|@LB@ 84 74@LB@@LB@@LB@Energy -10.26 kcal/mol@LB@Hybridization Energy -12.6611 kcal/mol@LB@Unfolding Energy - mRNA 1.90691 kcal/mol@LB@Unfolding Energy - sRNA 0.492259 kcal/mol@LB@@LB@Position - mRNA 236 -- 244@LB@Position - sRNA 75 -- 83@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 75 -- 81@LB@
60	0.01169	0.5385	b2441	eutB	-14.17	0.019414	238 -- 261	12 -- 34	ethanolamine ammonia-lyase large subunit heavy chain	_____________237______________________262\n_____________\|________________________\|\n5'-CUG...AUAUC_G_______AUG____________UGGCU...UGG-3'\n______________A_UUUAAGG___UAAAAGAGGUGC\n______________\|_\|\|:\|\|\|\|___\|\|\|\|\|\|\|\|\|\|\|\|\n______________U_AAGUUCC___AUUUUCUCCACG\n3'-CGC...GUCAC_G_______CA_____________GCGAG...AAG-5'\n_____________\|________________________\|\n_____________35_______________________11\n	255 -- 261	12 -- 18	-24.3693 kcal/mol	4.39141 kcal/mol	5.80707 kcal/mol	237 262@LB@ \| \|@LB@5'-CUG...AUAUC G AUG UGGCU...UGG-3'@LB@ A UUUAAGG UAAAAGAGGUGC@LB@ \| \|\|:\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|@LB@ U AAGUUCC AUUUUCUCCACG@LB@3'-CGC...GUCAC G CA GCGAG...AAG-5'@LB@ \| \|@LB@ 35 11@LB@@LB@@LB@Energy -14.17 kcal/mol@LB@Hybridization Energy -24.3693 kcal/mol@LB@Unfolding Energy - mRNA 4.39141 kcal/mol@LB@Unfolding Energy - sRNA 5.80707 kcal/mol@LB@@LB@Position - mRNA 238 -- 261@LB@Position - sRNA 12 -- 34@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 12 -- 18@LB@
77	0.01396	0.5385	b3644	yicC	-11.79	0.051421	238 -- 254	15 -- 31	UPF0701 family protein	_____________237_______________255\n_____________\|_________________\|\n5'-UCU...UGAAA________GAAU_____AGCGC...AAA-3'\n______________UCAAGGGU____GGGGG\n______________\|\|\|\|\|\|\|\|____:\|:\|\|\n______________AGUUCCCA____UCUCC\n3'-CGC...ACUGA________AUUU_____ACGGC...AAG-5'\n_____________\|_________________\|\n_____________32________________14\n	239 -- 245	24 -- 30	-20.4957 kcal/mol	5.4171 kcal/mol	3.28624 kcal/mol	237 255@LB@ \| \|@LB@5'-UCU...UGAAA GAAU AGCGC...AAA-3'@LB@ UCAAGGGU GGGGG@LB@ \|\|\|\|\|\|\|\| :\|:\|\|@LB@ AGUUCCCA UCUCC@LB@3'-CGC...ACUGA AUUU ACGGC...AAG-5'@LB@ \| \|@LB@ 32 14@LB@@LB@@LB@Energy -11.79 kcal/mol@LB@Hybridization Energy -20.4957 kcal/mol@LB@Unfolding Energy - mRNA 5.4171 kcal/mol@LB@Unfolding Energy - sRNA 3.28624 kcal/mol@LB@@LB@Position - mRNA 238 -- 254@LB@Position - sRNA 15 -- 31@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 24 -- 30@LB@
168	0.0298	0.5559	b0161	degP	-8.84	0.166335	239 -- 253	75 -- 88	serine endoprotease (protease Do) membrane-associated	_____________238_____________254\n_____________\|_______________\|\n5'-AUU...GCUCU_______G_U_____GUUAU...CGA-3'\n______________GAGUUUA_G_UUGGC\n______________:\|\|\|\|:\|_\|_\|\|\|\|\|\n______________UUCAAGU_C_AACCG\n3'-CGC...GCGUU_______G_______AAAUC...AAG-5'\n_____________\|_______________\|\n_____________89______________74\n	239 -- 245	82 -- 88	-14.9204 kcal/mol	5.56475 kcal/mol	0.515884 kcal/mol	238 254@LB@ \| \|@LB@5'-AUU...GCUCU G U GUUAU...CGA-3'@LB@ GAGUUUA G UUGGC@LB@ :\|\|\|\|:\| \| \|\|\|\|\|@LB@ UUCAAGU C AACCG@LB@3'-CGC...GCGUU G AAAUC...AAG-5'@LB@ \| \|@LB@ 89 74@LB@@LB@@LB@Energy -8.84 kcal/mol@LB@Hybridization Energy -14.9204 kcal/mol@LB@Unfolding Energy - mRNA 5.56475 kcal/mol@LB@Unfolding Energy - sRNA 0.515884 kcal/mol@LB@@LB@Position - mRNA 239 -- 253@LB@Position - sRNA 75 -- 88@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 82 -- 88@LB@
150	0.02548	0.5485	b0180	fabZ	-10.02	0.104939	240 -- 263	1 -- 24	(3R)-hydroxymyristol acyl carrier protein dehydratase	_____________239______________________264\n_____________\|________________________\|\n5'-AAA...AGAUU______CUUC______A_______CCGUU...AAG-3'\n______________UUAGAA____UGCCGC_CCGUUUC\n______________\|\|\|:\|\|____\|\|\|\|\|\|_\|\|\|\|\|\|\|\n______________AAUUUU____ACGGCG_GGCAAAG\n3'-CGC...UUCCC______CUCC______A_______-5'\n_____________\|_______________________\|\n_____________25______________________1\n	257 -- 263	1 -- 7	-23.7452 kcal/mol	3.39044 kcal/mol	10.3355 kcal/mol	239 264@LB@ \| \|@LB@5'-AAA...AGAUU CUUC A CCGUU...AAG-3'@LB@ UUAGAA UGCCGC CCGUUUC@LB@ \|\|\|:\|\| \|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ AAUUUU ACGGCG GGCAAAG@LB@3'-CGC...UUCCC CUCC A -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -10.02 kcal/mol@LB@Hybridization Energy -23.7452 kcal/mol@LB@Unfolding Energy - mRNA 3.39044 kcal/mol@LB@Unfolding Energy - sRNA 10.3355 kcal/mol@LB@@LB@Position - mRNA 240 -- 263@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 1 -- 7@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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