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
182	0.03197	0.5559	b0212	gloB	-7.96	0.231442	50 -- 71	56 -- 75	hydroxyacylglutathione hydrolase	_____________49_____________________72\n_____________\|______________________\|\n5'-UUG...AUACA_______GAACCA_________CUGGC...AGC-3'\n______________UUUUAGU______CGGGUUGAG\n______________:\|\|\|\|\|\|______\|\|:\|\|\|\|\|\|\n______________GAAAUCA______GCUCAACUC\n3'-CGC...CAACC_______AUAA___________UUUGA...AAG-5'\n_____________\|______________________\|\n_____________76_____________________55\n	65 -- 71	56 -- 62	-16.3693 kcal/mol	6.6953 kcal/mol	1.71204 kcal/mol	49 72@LB@ \| \|@LB@5'-UUG...AUACA GAACCA CUGGC...AGC-3'@LB@ UUUUAGU CGGGUUGAG@LB@ :\|\|\|\|\|\| \|\|:\|\|\|\|\|\|@LB@ GAAAUCA GCUCAACUC@LB@3'-CGC...CAACC AUAA UUUGA...AAG-5'@LB@ \| \|@LB@ 76 55@LB@@LB@@LB@Energy -7.96 kcal/mol@LB@Hybridization Energy -16.3693 kcal/mol@LB@Unfolding Energy - mRNA 6.6953 kcal/mol@LB@Unfolding Energy - sRNA 1.71204 kcal/mol@LB@@LB@Position - mRNA 50 -- 71@LB@Position - sRNA 56 -- 75@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 56 -- 62@LB@
6	0.001078	0.5385	b0849	grxA	-11.19	0.065759	209 -- 232	58 -- 81	glutaredoxin 1 redox coenzyme for ribonucleotide reductase (RNR1a)	_____________208______________________233\n_____________\|________________________\|\n5'-AGU...CAAAC____AU_______C__________CCCUU...AUC-3'\n______________CGUU__UUUUGGU_GUUCGGGUUG\n______________\|\|\|\|__:\|\|\|:\|\|_:\|\|\|\|:\|\|\|\|\n______________GCAA__GAAAUCA_UAAGCUCAAC\n3'-CGC...CAAGU____CC_______A__________UCUUU...AAG-5'\n_____________\|________________________\|\n_____________82_______________________57\n	226 -- 232	58 -- 64	-21.2762 kcal/mol	8.79419 kcal/mol	1.29619 kcal/mol	208 233@LB@ \| \|@LB@5'-AGU...CAAAC AU C CCCUU...AUC-3'@LB@ CGUU UUUUGGU GUUCGGGUUG@LB@ \|\|\|\| :\|\|\|:\|\| :\|\|\|\|:\|\|\|\|@LB@ GCAA GAAAUCA UAAGCUCAAC@LB@3'-CGC...CAAGU CC A UCUUU...AAG-5'@LB@ \| \|@LB@ 82 57@LB@@LB@@LB@Energy -11.19 kcal/mol@LB@Hybridization Energy -21.2762 kcal/mol@LB@Unfolding Energy - mRNA 8.79419 kcal/mol@LB@Unfolding Energy - sRNA 1.29619 kcal/mol@LB@@LB@Position - mRNA 209 -- 232@LB@Position - sRNA 58 -- 81@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 58 -- 64@LB@
35	0.006586	0.5385	b2351	gtrB	-12.36	0.040837	174 -- 213	48 -- 89	CPS-53 (KpLE1) prophage; bactoprenol glucosyl transferase	_____________173________________________________________214\n_____________\|__________________________________________\|\n5'-GCA...UAUUC_____________U______GG__G___AA___A__UA____UUGUA...AAG-3'\n______________AAAGUUCAU__UG_CUUUAG__AU_CGA__UGA_GA__UCUC\n______________\|\|\|\|\|\|\|\|:__\|\|_\|\|\|\|\|\|__\|\|_\|\|\|__\|\|\|_:\|__\|\|\|\|\n______________UUUCAAGUG__AC_GAAAUC__UA_GCU__ACU_UU__AGAG\n3'-CGC...GGCGU_________CA__C______AA__A___CA___C__UG____CUUUG...AAG-5'\n_____________\|__________________________________________\|\n_____________90_________________________________________47\n	176 -- 182	81 -- 87	-27.281 kcal/mol	10.5075 kcal/mol	4.41572 kcal/mol	173 214@LB@ \| \|@LB@5'-GCA...UAUUC U GG G AA A UA UUGUA...AAG-3'@LB@ AAAGUUCAU UG CUUUAG AU CGA UGA GA UCUC@LB@ \|\|\|\|\|\|\|\|: \|\| \|\|\|\|\|\| \|\| \|\|\| \|\|\| :\| \|\|\|\|@LB@ UUUCAAGUG AC GAAAUC UA GCU ACU UU AGAG@LB@3'-CGC...GGCGU CA C AA A CA C UG CUUUG...AAG-5'@LB@ \| \|@LB@ 90 47@LB@@LB@@LB@Energy -12.36 kcal/mol@LB@Hybridization Energy -27.281 kcal/mol@LB@Unfolding Energy - mRNA 10.5075 kcal/mol@LB@Unfolding Energy - sRNA 4.41572 kcal/mol@LB@@LB@Position - mRNA 174 -- 213@LB@Position - sRNA 48 -- 89@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 81 -- 87@LB@
104	0.0176	0.5385	b2788	gudX	-9.05	0.153387	171 -- 179	57 -- 65	glucarate dehydratase-related protein substrate unknown	_____________170_______180\n_____________\|_________\|\n5'-CGG...GCGUA_________AACCU...CAU-3'\n______________UCGAGUUGA\n______________\|\|\|\|\|\|\|\|\|\n______________AGCUCAACU\n3'-CGC...CAAUA_________CUUUG...AAG-5'\n_____________\|_________\|\n_____________66________56\n	173 -- 179	57 -- 63	-12.8916 kcal/mol	2.7095 kcal/mol	1.13183 kcal/mol	170 180@LB@ \| \|@LB@5'-CGG...GCGUA AACCU...CAU-3'@LB@ UCGAGUUGA@LB@ \|\|\|\|\|\|\|\|\|@LB@ AGCUCAACU@LB@3'-CGC...CAAUA CUUUG...AAG-5'@LB@ \| \|@LB@ 66 56@LB@@LB@@LB@Energy -9.05 kcal/mol@LB@Hybridization Energy -12.8916 kcal/mol@LB@Unfolding Energy - mRNA 2.7095 kcal/mol@LB@Unfolding Energy - sRNA 1.13183 kcal/mol@LB@@LB@Position - mRNA 171 -- 179@LB@Position - sRNA 57 -- 65@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 57 -- 63@LB@
176	0.03112	0.5559	b2536	hcaT	-7.63	0.261550	240 -- 259	67 -- 85	putative 3-phenylpropionic transporter	_____________239__________________260\n_____________\|____________________\|\n5'-UCG...GCUAU_____AUACUU_________CGGCA...GGA-3'\n______________UUCAC______UUUUAGUUA\n______________\|\|\|\|\|______:\|\|\|\|\|\|\|\|\n______________AAGUG______GAAAUCAAU\n3'-CGC...UUUUC_____CAACC__________AAGCU...AAG-5'\n_____________\|____________________\|\n_____________86___________________66\n	253 -- 259	67 -- 73	-10.0019 kcal/mol	1.80629 kcal/mol	0.569003 kcal/mol	239 260@LB@ \| \|@LB@5'-UCG...GCUAU AUACUU CGGCA...GGA-3'@LB@ UUCAC UUUUAGUUA@LB@ \|\|\|\|\| :\|\|\|\|\|\|\|\|@LB@ AAGUG GAAAUCAAU@LB@3'-CGC...UUUUC CAACC AAGCU...AAG-5'@LB@ \| \|@LB@ 86 66@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -10.0019 kcal/mol@LB@Unfolding Energy - mRNA 1.80629 kcal/mol@LB@Unfolding Energy - sRNA 0.569003 kcal/mol@LB@@LB@Position - mRNA 240 -- 259@LB@Position - sRNA 67 -- 85@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 67 -- 73@LB@
108	0.0187	0.5385	b1210	hemA	-9.14	0.148366	174 -- 184	75 -- 84	glutamyl tRNA reductase	_____________173_________185\n_____________\|___________\|\n5'-CCU...CCCUA__A________AUUAU...ACA-3'\n______________UC_ACGUUGGU\n______________\|\|_\|\|\|\|\|\|\|:\n______________AG_UGCAACCG\n3'-CGC...UUUCA___________AAAUC...AAG-5'\n_____________\|___________\|\n_____________85__________74\n	178 -- 184	75 -- 81	-12.935 kcal/mol	3.29275 kcal/mol	0.505918 kcal/mol	173 185@LB@ \| \|@LB@5'-CCU...CCCUA A AUUAU...ACA-3'@LB@ UC ACGUUGGU@LB@ \|\| \|\|\|\|\|\|\|:@LB@ AG UGCAACCG@LB@3'-CGC...UUUCA AAAUC...AAG-5'@LB@ \| \|@LB@ 85 74@LB@@LB@@LB@Energy -9.14 kcal/mol@LB@Hybridization Energy -12.935 kcal/mol@LB@Unfolding Energy - mRNA 3.29275 kcal/mol@LB@Unfolding Energy - sRNA 0.505918 kcal/mol@LB@@LB@Position - mRNA 174 -- 184@LB@Position - sRNA 75 -- 84@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 75 -- 81@LB@
187	0.03332	0.5559	b2019	hisG	-10.76	0.077976	170 -- 191	15 -- 34	ATP phosphoribosyltransferase	_____________169____________________192\n_____________\|______________________\|\n5'-UUU...AUAAC_G_____ACA____U_______AAUAA...AUC-3'\n______________G_UUCAG___GGUU_AAAGAGG\n______________:_\|\|\|\|:___\|\|\|\|_\|\|\|\|\|\|\|\n______________U_AAGUU___CCAA_UUUCUCC\n3'-CGC...GUCAC_G_____C______U_______ACGGC...AAG-5'\n_____________\|______________________\|\n_____________35_____________________14\n	185 -- 191	15 -- 21	-17.0816 kcal/mol	2.9882 kcal/mol	3.33044 kcal/mol	169 192@LB@ \| \|@LB@5'-UUU...AUAAC G ACA U AAUAA...AUC-3'@LB@ G UUCAG GGUU AAAGAGG@LB@ : \|\|\|\|: \|\|\|\| \|\|\|\|\|\|\|@LB@ U AAGUU CCAA UUUCUCC@LB@3'-CGC...GUCAC G C U ACGGC...AAG-5'@LB@ \| \|@LB@ 35 14@LB@@LB@@LB@Energy -10.76 kcal/mol@LB@Hybridization Energy -17.0816 kcal/mol@LB@Unfolding Energy - mRNA 2.9882 kcal/mol@LB@Unfolding Energy - sRNA 3.33044 kcal/mol@LB@@LB@Position - mRNA 170 -- 191@LB@Position - sRNA 15 -- 34@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 15 -- 21@LB@
75	0.01364	0.5385	b0107	hofB	-15.68	0.010425	272 -- 289	69 -- 87	T2SE secretion family protein; P-loop ATPase superfamily protein	_____________271_________________290\n_____________\|___________________\|\n5'-CCA...GAGGU_____________GG____CGAUG...CUU-3'\n______________GGUUCAUGUUG_C__UAGU\n______________:\|\|\|\|\|:\|\|\|\|_\|__\|\|\|\|\n______________UCAAGUGCAAC_G__AUCA\n3'-CGC...CGUUU___________C_AA____AUAAG...AAG-5'\n_____________\|___________________\|\n_____________88__________________68\n	276 -- 282	77 -- 83	-18.3354 kcal/mol	2.08484 kcal/mol	0.569189 kcal/mol	271 290@LB@ \| \|@LB@5'-CCA...GAGGU GG CGAUG...CUU-3'@LB@ GGUUCAUGUUG C UAGU@LB@ :\|\|\|\|\|:\|\|\|\| \| \|\|\|\|@LB@ UCAAGUGCAAC G AUCA@LB@3'-CGC...CGUUU C AA AUAAG...AAG-5'@LB@ \| \|@LB@ 88 68@LB@@LB@@LB@Energy -15.68 kcal/mol@LB@Hybridization Energy -18.3354 kcal/mol@LB@Unfolding Energy - mRNA 2.08484 kcal/mol@LB@Unfolding Energy - sRNA 0.569189 kcal/mol@LB@@LB@Position - mRNA 272 -- 289@LB@Position - sRNA 69 -- 87@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 77 -- 83@LB@
132	0.0226	0.5385	b2721	hycE	-8.05	0.224194	140 -- 148	71 -- 79	hydrogenase 3 large subunit	_____________139_______149\n_____________\|_________\|\n5'-UUC...UGGGU_________CAUUU...UGA-3'\n______________UUGGCUUUG\n______________\|\|\|\|\|\|\|\|:\n______________AACCGAAAU\n3'-CGC...AGUGC_________CAAUA...AAG-5'\n_____________\|_________\|\n_____________80________70\n	142 -- 148	71 -- 77	-10.5671 kcal/mol	2.29615 kcal/mol	0.222833 kcal/mol	139 149@LB@ \| \|@LB@5'-UUC...UGGGU CAUUU...UGA-3'@LB@ UUGGCUUUG@LB@ \|\|\|\|\|\|\|\|:@LB@ AACCGAAAU@LB@3'-CGC...AGUGC CAAUA...AAG-5'@LB@ \| \|@LB@ 80 70@LB@@LB@@LB@Energy -8.05 kcal/mol@LB@Hybridization Energy -10.5671 kcal/mol@LB@Unfolding Energy - mRNA 2.29615 kcal/mol@LB@Unfolding Energy - sRNA 0.222833 kcal/mol@LB@@LB@Position - mRNA 140 -- 148@LB@Position - sRNA 71 -- 79@LB@Position Seed - mRNA 142 -- 148@LB@Position Seed - sRNA 71 -- 77@LB@
2	0.0001834	0.3	b2729	hypD	-13.53	0.025234	75 -- 91	71 -- 87	hydrogenase maturation protein	_____________74________________92\n_____________\|_________________\|\n5'-CAG...GUACU___A_____________CCAUG...GCC-3'\n______________GGU_CACGUUGGCUUUG\n______________:\|\|_\|\|\|\|\|\|\|\|\|\|\|\|:\n______________UCA_GUGCAACCGAAAU\n3'-CGC...CGUUU___A_____________CAAUA...AAG-5'\n_____________\|_________________\|\n_____________88________________70\n	85 -- 91	71 -- 77	-22.1935 kcal/mol	8.09841 kcal/mol	0.562376 kcal/mol	74 92@LB@ \| \|@LB@5'-CAG...GUACU A CCAUG...GCC-3'@LB@ GGU CACGUUGGCUUUG@LB@ :\|\| \|\|\|\|\|\|\|\|\|\|\|\|:@LB@ UCA GUGCAACCGAAAU@LB@3'-CGC...CGUUU A CAAUA...AAG-5'@LB@ \| \|@LB@ 88 70@LB@@LB@@LB@Energy -13.53 kcal/mol@LB@Hybridization Energy -22.1935 kcal/mol@LB@Unfolding Energy - mRNA 8.09841 kcal/mol@LB@Unfolding Energy - sRNA 0.562376 kcal/mol@LB@@LB@Position - mRNA 75 -- 91@LB@Position - sRNA 71 -- 87@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 71 -- 77@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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