Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
93	0.00579	0.2147	b1256	ompW	-13.14	0.073154	206 -- 220	1 -- 16	outer membrane protein W	_____________205______________221\n_____________\|________________\|\n5'-GAC...AUGAA____UU__________GGCUU...CUG-3'\n______________AAAG__AA_CAGUGGC\n______________\|\|\|\|__\|\|_\|\|\|\|\|\|\|\n______________UUUC__UU_GUCACCG\n3'-UUU...UGUAG____UU__C_______-5'\n_____________\|_______________\|\n_____________17______________1\n	214 -- 220	1 -- 7	-16.0357 kcal/mol	1.55126 kcal/mol	1.34555 kcal/mol	205 221@LB@ \| \|@LB@5'-GAC...AUGAA UU GGCUU...CUG-3'@LB@ AAAG AA CAGUGGC@LB@ \|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ UUUC UU GUCACCG@LB@3'-UUU...UGUAG UU C -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -13.14 kcal/mol@LB@Hybridization Energy -16.0357 kcal/mol@LB@Unfolding Energy - mRNA 1.55126 kcal/mol@LB@Unfolding Energy - sRNA 1.34555 kcal/mol@LB@@LB@Position - mRNA 206 -- 220@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 1 -- 7@LB@
135	0.009724	0.2504	b1387	paaZ	-12.57	0.095542	174 -- 198	5 -- 30	oxepin-CoA hydrolase and 3-oxo-5 6-dehydrosuberyl-CoA semialdehyde dehydrogenase	_____________173_________________________199\n_____________\|___________________________\|\n5'-UAA...CAACA______U_AA_____U___________CGAUG...AAG-3'\n______________GAAAUG_G__ACAUC___GGAGAGUAG\n______________:\|\|\|\|\|_\|__\|\|\|\|\|___\|:\|:\|\|:\|\|\n______________UUUUAC_C__UGUAG___CUUUUCGUC\n3'-UUU...AGGUG________CC_____UUU_________ACCG-5'\n_____________\|___________________________\|\n_____________31__________________________4\n	192 -- 198	5 -- 11	-19.0129 kcal/mol	3.93627 kcal/mol	2.50278 kcal/mol	173 199@LB@ \| \|@LB@5'-UAA...CAACA U AA U CGAUG...AAG-3'@LB@ GAAAUG G ACAUC GGAGAGUAG@LB@ :\|\|\|\|\| \| \|\|\|\|\| \|:\|:\|\|:\|\|@LB@ UUUUAC C UGUAG CUUUUCGUC@LB@3'-UUU...AGGUG CC UUU ACCG-5'@LB@ \| \|@LB@ 31 4@LB@@LB@@LB@Energy -12.57 kcal/mol@LB@Hybridization Energy -19.0129 kcal/mol@LB@Unfolding Energy - mRNA 3.93627 kcal/mol@LB@Unfolding Energy - sRNA 2.50278 kcal/mol@LB@@LB@Position - mRNA 174 -- 198@LB@Position - sRNA 5 -- 30@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 5 -- 11@LB@
15	0.0006403	0.1243	b0178	skp	-17.37	0.006465	90 -- 106	1 -- 17	periplasmic chaperone	_____________89________________107\n_____________\|_________________\|\n5'-CUC...CUCCA________U________AGUGU...UCC-3'\n______________CAAAGGAA_GUAGUGGU\n______________\|\|\|\|\|:\|\|_\|:\|\|\|\|\|:\n______________GUUUCUUU_CGUCACCG\n3'-UUU...CUGUA________U________-5'\n_____________\|________________\|\n_____________18_______________1\n	100 -- 106	1 -- 7	-21.6829 kcal/mol	2.87621 kcal/mol	1.43853 kcal/mol	89 107@LB@ \| \|@LB@5'-CUC...CUCCA U AGUGU...UCC-3'@LB@ CAAAGGAA GUAGUGGU@LB@ \|\|\|\|\|:\|\| \|:\|\|\|\|\|:@LB@ GUUUCUUU CGUCACCG@LB@3'-UUU...CUGUA U -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -17.37 kcal/mol@LB@Hybridization Energy -21.6829 kcal/mol@LB@Unfolding Energy - mRNA 2.87621 kcal/mol@LB@Unfolding Energy - sRNA 1.43853 kcal/mol@LB@@LB@Position - mRNA 90 -- 106@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 1 -- 7@LB@
78	0.004634	0.2062	b1601	tqsA	-18.27	0.003423	191 -- 205	1 -- 25	pheromone AI-2 transporter	_____________190_______________________206\n_____________\|_________________________\|\n5'-AUU...AAAAC_________________________AAAGC...UCA-3'\n______________GGGGACA_________AGCA_UGGC\n______________\|\|\|\|\|\|\|_________\|\|\|\|_\|\|\|\|\n______________CCCCUGU_________UCGU_ACCG\n3'-UUU...UUUUA_______AGUUUCUUU____C____-5'\n_____________\|________________________\|\n_____________26_______________________1\n	191 -- 197	19 -- 25	-23.2822 kcal/mol	2.49324 kcal/mol	2.51748 kcal/mol	190 206@LB@ \| \|@LB@5'-AUU...AAAAC AAAGC...UCA-3'@LB@ GGGGACA AGCA UGGC@LB@ \|\|\|\|\|\|\| \|\|\|\| \|\|\|\|@LB@ CCCCUGU UCGU ACCG@LB@3'-UUU...UUUUA AGUUUCUUU C -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -18.27 kcal/mol@LB@Hybridization Energy -23.2822 kcal/mol@LB@Unfolding Energy - mRNA 2.49324 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 191 -- 205@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 19 -- 25@LB@
91	0.005641	0.2147	b3956	ppc	-14.82	0.030673	242 -- 282	2 -- 37	phosphoenolpyruvate carboxylase	_____________241_________________________________________283\n_____________\|___________________________________________\|\n5'-CUU...AGUAU____G________CU____GAAAC_________U_____U___GAGAA...AAC-3'\n______________GCUC_GCAAAGUG__GGGA_____CAUCAAGGA___GCG_UGG\n______________\|\|\|\|_:\|\|\|\|:\|\|__\|\|\|\|_____\|\|\|\|\|\|:\|\|___\|\|:_\|\|\|\n______________CGAG_UGUUUUAC__CCCU_____GUAGUUUCU___CGU_ACC\n3'-UUU...CUACC____G____________________________UUU___C___G-5'\n_____________\|___________________________________________\|\n_____________38__________________________________________1\n	268 -- 274	12 -- 18	-37.6415 kcal/mol	13.2441 kcal/mol	9.57751 kcal/mol	241 283@LB@ \| \|@LB@5'-CUU...AGUAU G CU GAAAC U U GAGAA...AAC-3'@LB@ GCUC GCAAAGUG GGGA CAUCAAGGA GCG UGG@LB@ \|\|\|\| :\|\|\|\|:\|\| \|\|\|\| \|\|\|\|\|\|:\|\| \|\|: \|\|\|@LB@ CGAG UGUUUUAC CCCU GUAGUUUCU CGU ACC@LB@3'-UUU...CUACC G UUU C G-5'@LB@ \| \|@LB@ 38 1@LB@@LB@@LB@Energy -14.82 kcal/mol@LB@Hybridization Energy -37.6415 kcal/mol@LB@Unfolding Energy - mRNA 13.2441 kcal/mol@LB@Unfolding Energy - sRNA 9.57751 kcal/mol@LB@@LB@Position - mRNA 242 -- 282@LB@Position - sRNA 2 -- 37@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 12 -- 18@LB@
12	0.0004023	0.1087	b3176	glmM	-16.74	0.009770	131 -- 153	1 -- 22	phosphoglucosamine mutase	_____________130_____________________154\n_____________\|_______________________\|\n5'-GUU...UUCAU_____________CC____AA__GAUGC...CGG-3'\n______________GACGUCAAAGAAA__GUAG__GC\n______________\|\|\|:\|\|\|\|\|\|\|\|\|__\|:\|\|__\|\|\n______________CUGUAGUUUCUUU__CGUC__CG\n3'-UUU...UACCC_____________U_____AC__-5'\n_____________\|______________________\|\n_____________23_____________________1\n	137 -- 143	10 -- 16	-21.6768 kcal/mol	3.39473 kcal/mol	1.54023 kcal/mol	130 154@LB@ \| \|@LB@5'-GUU...UUCAU CC AA GAUGC...CGG-3'@LB@ GACGUCAAAGAAA GUAG GC@LB@ \|\|\|:\|\|\|\|\|\|\|\|\| \|:\|\| \|\|@LB@ CUGUAGUUUCUUU CGUC CG@LB@3'-UUU...UACCC U AC -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -16.74 kcal/mol@LB@Hybridization Energy -21.6768 kcal/mol@LB@Unfolding Energy - mRNA 3.39473 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 131 -- 153@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 137 -- 143@LB@Position Seed - sRNA 10 -- 16@LB@
29	0.00125	0.1512	b2499	purM	-15.92	0.016248	173 -- 203	3 -- 34	phosphoribosylaminoimidazole synthetase	_____________172____________________________________204\n_____________\|______________________________________\|\n5'-UAU...UUCUA_______UAACGC________CC_______________ACCGA...CGC-3'\n______________CCGCAAG______GUGGGGAC_________AAGCAGUG\n______________\|\|:\|\|\|:______:\|\|\|\|\|\|\|_________\|\|\|\|\|\|\|\|\n______________GGUGUUU______UACCCCUG_________UUCGUCAC\n3'-UUU...CCCGA_____________________UAGUUUCUU________CG-5'\n_____________\|______________________________________\|\n_____________35_____________________________________2\n	197 -- 203	3 -- 9	-29.7141 kcal/mol	9.52212 kcal/mol	4.26884 kcal/mol	172 204@LB@ \| \|@LB@5'-UAU...UUCUA UAACGC CC ACCGA...CGC-3'@LB@ CCGCAAG GUGGGGAC AAGCAGUG@LB@ \|\|:\|\|\|: :\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ GGUGUUU UACCCCUG UUCGUCAC@LB@3'-UUU...CCCGA UAGUUUCUU CG-5'@LB@ \| \|@LB@ 35 2@LB@@LB@@LB@Energy -15.92 kcal/mol@LB@Hybridization Energy -29.7141 kcal/mol@LB@Unfolding Energy - mRNA 9.52212 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 173 -- 203@LB@Position - sRNA 3 -- 34@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 3 -- 9@LB@
60	0.003101	0.1789	b1849	purT	-10.92	0.194410	188 -- 196	17 -- 25	phosphoribosylglycinamide formyltransferase 2	_____________187_______197\n_____________\|_________\|\n5'-UUU...AAUCA_________CGUUA...GUC-3'\n______________GGGGAUAUU\n______________\|\|\|\|\|:\|\|:\n______________CCCCUGUAG\n3'-UUU...UUUUA_________UUUCU...CCG-5'\n_____________\|_________\|\n_____________26________16\n	190 -- 196	17 -- 23	-14.1846 kcal/mol	2.60139 kcal/mol	0.664736 kcal/mol	187 197@LB@ \| \|@LB@5'-UUU...AAUCA CGUUA...GUC-3'@LB@ GGGGAUAUU@LB@ \|\|\|\|\|:\|\|:@LB@ CCCCUGUAG@LB@3'-UUU...UUUUA UUUCU...CCG-5'@LB@ \| \|@LB@ 26 16@LB@@LB@@LB@Energy -10.92 kcal/mol@LB@Hybridization Energy -14.1846 kcal/mol@LB@Unfolding Energy - mRNA 2.60139 kcal/mol@LB@Unfolding Energy - sRNA 0.664736 kcal/mol@LB@@LB@Position - mRNA 188 -- 196@LB@Position - sRNA 17 -- 25@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 17 -- 23@LB@
154	0.01125	0.2504	b3412	bioH	-12.84	0.084220	262 -- 288	1 -- 28	pimeloyl-ACP methyl ester carboxylesterase	_____________261__________________________289\n_____________\|____________________________\|\n5'-GGC...GCACG_________UGAAUGCC___________GUUGC...ACG-3'\n______________GAUGGGGAC________GAAGU_GUGGC\n______________:\|\|\|\|\|\|\|\|________:\|\|\|:_\|\|\|\|\|\n______________UUACCCCUG________UUUCG_CACCG\n3'-UUU...GUGUU_________UAGUUUCU_____U_____-5'\n_____________\|___________________________\|\n_____________29__________________________1\n	264 -- 270	20 -- 26	-27.647 kcal/mol	12.2839 kcal/mol	2.519 kcal/mol	261 289@LB@ \| \|@LB@5'-GGC...GCACG UGAAUGCC GUUGC...ACG-3'@LB@ GAUGGGGAC GAAGU GUGGC@LB@ :\|\|\|\|\|\|\|\| :\|\|\|: \|\|\|\|\|@LB@ UUACCCCUG UUUCG CACCG@LB@3'-UUU...GUGUU UAGUUUCU U -5'@LB@ \| \|@LB@ 29 1@LB@@LB@@LB@Energy -12.84 kcal/mol@LB@Hybridization Energy -27.647 kcal/mol@LB@Unfolding Energy - mRNA 12.2839 kcal/mol@LB@Unfolding Energy - sRNA 2.519 kcal/mol@LB@@LB@Position - mRNA 262 -- 288@LB@Position - sRNA 1 -- 28@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 20 -- 26@LB@
11	0.0003708	0.1087	b4201	priB	-14.90	0.029310	176 -- 193	6 -- 26	primosomal protein N	_____________175___________________194\n_____________\|_____________________\|\n5'-AGG...GAAGC__________U__________AUUUC...AUC-3'\n______________UGGGGAU_UC___GAAGAGUA\n______________\|\|\|\|\|\|:_\|\|___\|\|\|:\|\|:\|\n______________ACCCCUG_AG___CUUUUCGU\n3'-UUU...GUUUU_______U__UUU________CACCG-5'\n_____________\|_____________________\|\n_____________27____________________5\n	187 -- 193	6 -- 12	-19.0189 kcal/mol	3.41067 kcal/mol	0.706421 kcal/mol	175 194@LB@ \| \|@LB@5'-AGG...GAAGC U AUUUC...AUC-3'@LB@ UGGGGAU UC GAAGAGUA@LB@ \|\|\|\|\|\|: \|\| \|\|\|:\|\|:\|@LB@ ACCCCUG AG CUUUUCGU@LB@3'-UUU...GUUUU U UUU CACCG-5'@LB@ \| \|@LB@ 27 5@LB@@LB@@LB@Energy -14.90 kcal/mol@LB@Hybridization Energy -19.0189 kcal/mol@LB@Unfolding Energy - mRNA 3.41067 kcal/mol@LB@Unfolding Energy - sRNA 0.706421 kcal/mol@LB@@LB@Position - mRNA 176 -- 193@LB@Position - sRNA 6 -- 26@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 6 -- 12@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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