Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
146	0.01559	0.358	b4394	yjjX	-8.60	0.483218	101 -- 114	123 -- 137	non-canonical purine NTP phosphatase ITPase/XTPase		_____________100__________________________________115\n_____________\|____________________________________\|\n5'-UGC...AAUCC______A______________UC________UU___CGAGA...CAU-3'\n______________CGCUAA_AUUCAG__GC_CAU__UGCAGGCA__UCA\n______________\|:\|:\|\|_\|:\|\|\|\|__:\|_\|\|\|__\|\|\|\|\|\|\|\|__\|\|\|\n______________GUGGUU_UGAGUC__UG_GUA__ACGUCCGU__AGU\n3'-UUU...AAAAU______A______AG__U___CU________UC___UGAAA...UAG-5'\n_____________\|____________________________________\|\n_____________138__________________________________122\n	254 -- 260	156 -- 162	-32.2061 kcal/mol	8.98762 kcal/mol	12.5635 kcal/mol	100 115@LB@ \| \|@LB@5'-UGC...AAUCC A UC UU CGAGA...CAU-3'@LB@ CGCUAA AUUCAG GC CAU UGCAGGCA UCA@LB@ \|:\|:\|\| \|:\|\|\|\| :\| \|\|\| \|\|\|\|\|\|\|\| \|\|\|@LB@ GUGGUU UGAGUC UG GUA ACGUCCGU AGU@LB@3'-UUU...AAAAU A AG U CU UC UGAAA...UAG-5'@LB@ \| \|@LB@ 138 122@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -32.2061 kcal/mol@LB@Unfolding Energy - mRNA 8.98762 kcal/mol@LB@Unfolding Energy - sRNA 12.5635 kcal/mol@LB@@LB@Position - mRNA 101 -- 114@LB@Position - sRNA 123 -- 137@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 156 -- 162@LB@
61	0.006025	0.3261	b4330	yjiH	-10.68	0.204041	214 -- 227	80 -- 92	nucleoside recognition pore and gate family putative inner membrane transporter		_____________213______228\n_____________\|________\|\n5'-ACU...ACAAG________GUAGC...CCG-3'\n______________GGGAUGCU\n______________\|\|\|\|:\|\|\|\n______________CCCUGCGA\n3'-UUU...CAACA________AUUGG...UAG-5'\n_____________\|________\|\n_____________93_______79\n	215 -- 221	85 -- 91	-14.2816 kcal/mol	2.08889 kcal/mol	5.76908 kcal/mol	213 228@LB@ \| \|@LB@5'-ACU...ACAAG GUAGC...CCG-3'@LB@ GGGAUGCU@LB@ \|\|\|\|:\|\|\|@LB@ CCCUGCGA@LB@3'-UUU...CAACA AUUGG...UAG-5'@LB@ \| \|@LB@ 93 79@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -14.2816 kcal/mol@LB@Unfolding Energy - mRNA 2.08889 kcal/mol@LB@Unfolding Energy - sRNA 5.76908 kcal/mol@LB@@LB@Position - mRNA 214 -- 227@LB@Position - sRNA 80 -- 92@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 85 -- 91@LB@
56	0.005619	0.3247	b2781	mazG	-9.54	0.334798	182 -- 193	141 -- 152	nucleoside triphosphate pyrophosphohydrolase		_____________181__________194\n_____________\|____________\|\n5'-UGA...ACCCG____________CAAUU...CGC-3'\n______________CAAUUUUCAGGA\n______________\|\|\|:\|\|\|\|\|\|:\|\n______________GUUGAAAGUCUU\n3'-UUU...GUUCA____________AACGC...UAG-5'\n_____________\|____________\|\n_____________153__________140\n	187 -- 193	141 -- 147	-13.182 kcal/mol	1.77322 kcal/mol	1.81388 kcal/mol	181 194@LB@ \| \|@LB@5'-UGA...ACCCG CAAUU...CGC-3'@LB@ CAAUUUUCAGGA@LB@ \|\|\|:\|\|\|\|\|\|:\|@LB@ GUUGAAAGUCUU@LB@3'-UUU...GUUCA AACGC...UAG-5'@LB@ \| \|@LB@ 153 140@LB@@LB@@LB@Energy -9.54 kcal/mol@LB@Hybridization Energy -13.182 kcal/mol@LB@Unfolding Energy - mRNA 1.77322 kcal/mol@LB@Unfolding Energy - sRNA 1.81388 kcal/mol@LB@@LB@Position - mRNA 182 -- 193@LB@Position - sRNA 141 -- 152@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 141 -- 147@LB@
15	0.0008498	0.1886	b4254	argI	-15.11	0.025648	62 -- 84	167 -- 185	ornithine carbamoyltransferase 1	b0273	_____________61______________________85\n_____________\|_______________________\|\n5'-UUC...GUCCU__________UUAUU________CCACU...AUA-3'\n______________GCCGAUACUC_____GUCACACA\n______________:\|\|:\|\|\|\|\|\|_____\|\|\|\|\|\|\|\|\n______________UGGUUAUGAG_____CAGUGUGU\n3'-UUU...AAAUG__________U____________ACUAC...UAG-5'\n_____________\|_______________________\|\n_____________186_____________________166\n	78 -- 84	167 -- 173	-24.735 kcal/mol	3.62809 kcal/mol	5.02083 kcal/mol	61 85@LB@ \| \|@LB@5'-UUC...GUCCU UUAUU CCACU...AUA-3'@LB@ GCCGAUACUC GUCACACA@LB@ :\|\|:\|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ UGGUUAUGAG CAGUGUGU@LB@3'-UUU...AAAUG U ACUAC...UAG-5'@LB@ \| \|@LB@ 186 166@LB@@LB@@LB@Energy -15.11 kcal/mol@LB@Hybridization Energy -24.735 kcal/mol@LB@Unfolding Energy - mRNA 3.62809 kcal/mol@LB@Unfolding Energy - sRNA 5.02083 kcal/mol@LB@@LB@Position - mRNA 62 -- 84@LB@Position - sRNA 167 -- 185@LB@Position Seed - mRNA 78 -- 84@LB@Position Seed - sRNA 167 -- 173@LB@
11	0.0006963	0.1842	b1739	osmE	-13.14	0.065080	250 -- 260	194 -- 204	osmotically-inducible lipoprotein		_____________249_________261\n_____________\|___________\|\n5'-GAA...AACCA___________UGUAC...AGC-3'\n______________UGCUGGCGGGU\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________ACGACCGCCCA\n3'-UUU...AUUAG___________CUAAA...UAG-5'\n_____________\|___________\|\n_____________205_________193\n	254 -- 260	194 -- 200	-22.742 kcal/mol	5.67651 kcal/mol	8.00138 kcal/mol	249 261@LB@ \| \|@LB@5'-GAA...AACCA UGUAC...AGC-3'@LB@ UGCUGGCGGGU@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ ACGACCGCCCA@LB@3'-UUU...AUUAG CUAAA...UAG-5'@LB@ \| \|@LB@ 205 193@LB@@LB@@LB@Energy -13.14 kcal/mol@LB@Hybridization Energy -22.742 kcal/mol@LB@Unfolding Energy - mRNA 5.67651 kcal/mol@LB@Unfolding Energy - sRNA 8.00138 kcal/mol@LB@@LB@Position - mRNA 250 -- 260@LB@Position - sRNA 194 -- 204@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 194 -- 200@LB@
68	0.00659	0.3261	b4080	mdtP	-14.15	0.040423	195 -- 221	144 -- 172	outer membrane factor of efflux pump		_____________194_______________________________222\n_____________\|_________________________________\|\n5'-CUG...CAAGG__C_____A________AUC_____________CGUCU...CUC-3'\n______________AG_CACGC_AUGAU_CA_____GUCAACUUUCA\n______________\|\|_\|\|\|:\|_\|\|\|\|\|_\|\|_____\|\|\|\|\|\|\|\|\|\|\|\n______________UC_GUGUG_UACUA_GU_____CAGUUGAAAGU\n3'-UUU...AUGAG__A___________C__CCGUU___________CUUAA...UAG-5'\n_____________\|_________________________________\|\n_____________173_______________________________143\n	215 -- 221	144 -- 150	-24.8993 kcal/mol	3.71866 kcal/mol	8.07675 kcal/mol	194 222@LB@ \| \|@LB@5'-CUG...CAAGG C A AUC CGUCU...CUC-3'@LB@ AG CACGC AUGAU CA GUCAACUUUCA@LB@ \|\| \|\|\|:\| \|\|\|\|\| \|\| \|\|\|\|\|\|\|\|\|\|\|@LB@ UC GUGUG UACUA GU CAGUUGAAAGU@LB@3'-UUU...AUGAG A C CCGUU CUUAA...UAG-5'@LB@ \| \|@LB@ 173 143@LB@@LB@@LB@Energy -14.15 kcal/mol@LB@Hybridization Energy -24.8993 kcal/mol@LB@Unfolding Energy - mRNA 3.71866 kcal/mol@LB@Unfolding Energy - sRNA 8.07675 kcal/mol@LB@@LB@Position - mRNA 195 -- 221@LB@Position - sRNA 144 -- 172@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 144 -- 150@LB@
143	0.01531	0.3575	b1641	slyB	-10.83	0.190300	158 -- 167	83 -- 92	outer membrane lipoprotein		_____________157____________________________168\n_____________\|______________________________\|\n5'-CCG...UCACA_______U______UGAC____AGG_____UUGCG...AAG-3'\n______________UAUGCCA_AUACUU____CAUG___GAUGC\n______________\|\|::\|\|\|_\|\|\|\|\|:____\|\|::___\|\|\|\|\|\n______________AUGUGGU_UAUGAG____GUGU___CUACG\n3'-UUU...CUAAA______________UCA_____GUA_____UCCGU...UAG-5'\n_____________\|______________________________\|\n_____________93_____________________________82\n	135 -- 141	182 -- 188	-20.8318 kcal/mol	7.22081 kcal/mol	7.72227 kcal/mol	157 168@LB@ \| \|@LB@5'-CCG...UCACA U UGAC AGG UUGCG...AAG-3'@LB@ UAUGCCA AUACUU CAUG GAUGC@LB@ \|\|::\|\|\| \|\|\|\|\|: \|\|:: \|\|\|\|\|@LB@ AUGUGGU UAUGAG GUGU CUACG@LB@3'-UUU...CUAAA UCA GUA UCCGU...UAG-5'@LB@ \| \|@LB@ 93 82@LB@@LB@@LB@Energy -10.83 kcal/mol@LB@Hybridization Energy -20.8318 kcal/mol@LB@Unfolding Energy - mRNA 7.22081 kcal/mol@LB@Unfolding Energy - sRNA 7.72227 kcal/mol@LB@@LB@Position - mRNA 158 -- 167@LB@Position - sRNA 83 -- 92@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 182 -- 188@LB@
98	0.01073	0.3575	b0424	yajL	-11.45	0.143367	14 -- 29	155 -- 170	oxidative-stress-resistance chaperone		_____________13_______________30\n_____________\|________________\|\n5'-AGA...GUGAU________________UUGAU...CCA-3'\n______________UACGUGAUGCAGGUGA\n______________:\|\|:\|\|\|\|\|\|\|\|\|::\|\n______________GUGUACUACGUCCGUU\n3'-UUU...UCAGU________________CAGUU...UAG-5'\n_____________\|________________\|\n_____________171______________154\n	22 -- 28	156 -- 162	-24.1359 kcal/mol	6.48358 kcal/mol	7.06607 kcal/mol	13 30@LB@ \| \|@LB@5'-AGA...GUGAU UUGAU...CCA-3'@LB@ UACGUGAUGCAGGUGA@LB@ :\|\|:\|\|\|\|\|\|\|\|\|::\|@LB@ GUGUACUACGUCCGUU@LB@3'-UUU...UCAGU CAGUU...UAG-5'@LB@ \| \|@LB@ 171 154@LB@@LB@@LB@Energy -11.45 kcal/mol@LB@Hybridization Energy -24.1359 kcal/mol@LB@Unfolding Energy - mRNA 6.48358 kcal/mol@LB@Unfolding Energy - sRNA 7.06607 kcal/mol@LB@@LB@Position - mRNA 14 -- 29@LB@Position - sRNA 155 -- 170@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 156 -- 162@LB@
72	0.007293	0.3408	b3240	aaeB	-15.57	0.020683	172 -- 248	45 -- 133	p-hydroxybenzoic acid efflux system component		_____________171________________249\n_____________\|__________________\|\n5'-ACU...ACAUA__________________CUGGC...UGG-3'\n______________UUCGCU_UUGCGGUAAAA\n______________\|\|\|\|\|\|_\|:\|\|\|\|\|\|\|\|\|\n______________AAGCGA_AGCGCCAUUUU\n3'-UUU...UGUUG______C___________AUCAC...UAG-5'\n_____________\|__________________\|\n_____________134________________44\n	240 -- 246	47 -- 53	-22.573 kcal/mol	5.7072 kcal/mol	6.14031 kcal/mol	171 249@LB@ \| \|@LB@5'-ACU...ACAUA CUGGC...UGG-3'@LB@ UUCGCU UUGCGGUAAAA@LB@ \|\|\|\|\|\| \|:\|\|\|\|\|\|\|\|\|@LB@ AAGCGA AGCGCCAUUUU@LB@3'-UUU...UGUUG C AUCAC...UAG-5'@LB@ \| \|@LB@ 134 44@LB@@LB@@LB@Energy -15.57 kcal/mol@LB@Hybridization Energy -22.573 kcal/mol@LB@Unfolding Energy - mRNA 5.7072 kcal/mol@LB@Unfolding Energy - sRNA 6.14031 kcal/mol@LB@@LB@Position - mRNA 172 -- 248@LB@Position - sRNA 45 -- 133@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 47 -- 53@LB@
141	0.01524	0.3575	b0133	panC	-11.57	0.136229	4 -- 24	142 -- 162	pantothenate synthetase		_____________3_________25\n_____________\|_________\|\n5'-GGC...ACCGG_________UCCUA...UGC-3'\n______________CGGUCACAU\n______________\|:\|\|\|\|\|\|:\n______________GUCAGUGUG\n3'-UUU...UAUGA_________UACUA...UAG-5'\n_____________\|_________\|\n_____________163_______141\n	65 -- 71	168 -- 174	-12.1402 kcal/mol	2.67616 kcal/mol	0.276974 kcal/mol	3 25@LB@ \| \|@LB@5'-GGC...ACCGG UCCUA...UGC-3'@LB@ CGGUCACAU@LB@ \|:\|\|\|\|\|\|:@LB@ GUCAGUGUG@LB@3'-UUU...UAUGA UACUA...UAG-5'@LB@ \| \|@LB@ 163 141@LB@@LB@@LB@Energy -11.57 kcal/mol@LB@Hybridization Energy -12.1402 kcal/mol@LB@Unfolding Energy - mRNA 2.67616 kcal/mol@LB@Unfolding Energy - sRNA 0.276974 kcal/mol@LB@@LB@Position - mRNA 4 -- 24@LB@Position - sRNA 142 -- 162@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 168 -- 174@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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