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
197	0.0346	0.5559	b2829	ptsP	-9.94	0.108120	103 -- 113	80 -- 90	PEP-protein phosphotransferase enzyme I; GAF domain containing protein	_____________102_________114\n_____________\|___________\|\n5'-CCA...AAUGA___________AGUGU...UGG-3'\n______________AAGAGUUCGCG\n______________\|\|:\|\|\|\|\|:\|\|\n______________UUUUCAAGUGC\n3'-CGC...AGGCG___________AACCG...AAG-5'\n_____________\|___________\|\n_____________91__________79\n	107 -- 113	80 -- 86	-13.2227 kcal/mol	2.77203 kcal/mol	0.506776 kcal/mol	102 114@LB@ \| \|@LB@5'-CCA...AAUGA AGUGU...UGG-3'@LB@ AAGAGUUCGCG@LB@ \|\|:\|\|\|\|\|:\|\|@LB@ UUUUCAAGUGC@LB@3'-CGC...AGGCG AACCG...AAG-5'@LB@ \| \|@LB@ 91 79@LB@@LB@@LB@Energy -9.94 kcal/mol@LB@Hybridization Energy -13.2227 kcal/mol@LB@Unfolding Energy - mRNA 2.77203 kcal/mol@LB@Unfolding Energy - sRNA 0.506776 kcal/mol@LB@@LB@Position - mRNA 103 -- 113@LB@Position - sRNA 80 -- 90@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 80 -- 86@LB@
131	0.02244	0.5385	b1713	pheT	-10.81	0.076409	64 -- 80	73 -- 89	phenylalanine tRNA synthetase beta subunit	_____________63________________81\n_____________\|_________________\|\n5'-CUG...ACCCG_________UC______CGCCU...ACG-3'\n______________GAAGUUUAC__UGGUUU\n______________:\|\|\|\|\|:\|\|__\|\|\|:\|\|\n______________UUUCAAGUG__ACCGAA\n3'-CGC...GGCGU_________CA______AUCAA...AAG-5'\n_____________\|_________________\|\n_____________90________________72\n	66 -- 72	81 -- 87	-14.6363 kcal/mol	3.30516 kcal/mol	0.517627 kcal/mol	63 81@LB@ \| \|@LB@5'-CUG...ACCCG UC CGCCU...ACG-3'@LB@ GAAGUUUAC UGGUUU@LB@ :\|\|\|\|\|:\|\| \|\|\|:\|\|@LB@ UUUCAAGUG ACCGAA@LB@3'-CGC...GGCGU CA AUCAA...AAG-5'@LB@ \| \|@LB@ 90 72@LB@@LB@@LB@Energy -10.81 kcal/mol@LB@Hybridization Energy -14.6363 kcal/mol@LB@Unfolding Energy - mRNA 3.30516 kcal/mol@LB@Unfolding Energy - sRNA 0.517627 kcal/mol@LB@@LB@Position - mRNA 64 -- 80@LB@Position - sRNA 73 -- 89@LB@Position Seed - mRNA 66 -- 72@LB@Position Seed - sRNA 81 -- 87@LB@
42	0.008798	0.5385	b0087	mraY	-9.88	0.111048	142 -- 153	79 -- 90	phospho-N-acetylmuramoyl-pentapeptide transferase	_____________141__________154\n_____________\|____________\|\n5'-GAC...UAGUU____________AGUGC...CGC-3'\n______________AAGGGUUCACGU\n______________\|\|::\|\|\|\|\|\|\|\|\n______________UUUUCAAGUGCA\n3'-CGC...AGGCG____________ACCGA...AAG-5'\n_____________\|____________\|\n_____________91___________78\n	147 -- 153	79 -- 85	-14.1224 kcal/mol	3.73912 kcal/mol	0.506924 kcal/mol	141 154@LB@ \| \|@LB@5'-GAC...UAGUU AGUGC...CGC-3'@LB@ AAGGGUUCACGU@LB@ \|\|::\|\|\|\|\|\|\|\|@LB@ UUUUCAAGUGCA@LB@3'-CGC...AGGCG ACCGA...AAG-5'@LB@ \| \|@LB@ 91 78@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -14.1224 kcal/mol@LB@Unfolding Energy - mRNA 3.73912 kcal/mol@LB@Unfolding Energy - sRNA 0.506924 kcal/mol@LB@@LB@Position - mRNA 142 -- 153@LB@Position - sRNA 79 -- 90@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 79 -- 85@LB@
36	0.006672	0.5385	b3956	ppc	-10.31	0.093393	270 -- 282	76 -- 88	phosphoenolpyruvate carboxylase	_____________269___________283\n_____________\|_____________\|\n5'-CUU...CCAUC___GA________GAGAA...AAC-3'\n______________AAG__UGCGUUGG\n______________\|\|\|__::\|\|\|\|\|\|\n______________UUC__GUGCAACC\n3'-CGC...GCGUU___AA________GAAAU...AAG-5'\n_____________\|_____________\|\n_____________89____________75\n	276 -- 282	76 -- 82	-12.0501 kcal/mol	1.22517 kcal/mol	0.512479 kcal/mol	269 283@LB@ \| \|@LB@5'-CUU...CCAUC GA GAGAA...AAC-3'@LB@ AAG UGCGUUGG@LB@ \|\|\| ::\|\|\|\|\|\|@LB@ UUC GUGCAACC@LB@3'-CGC...GCGUU AA GAAAU...AAG-5'@LB@ \| \|@LB@ 89 75@LB@@LB@@LB@Energy -10.31 kcal/mol@LB@Hybridization Energy -12.0501 kcal/mol@LB@Unfolding Energy - mRNA 1.22517 kcal/mol@LB@Unfolding Energy - sRNA 0.512479 kcal/mol@LB@@LB@Position - mRNA 270 -- 282@LB@Position - sRNA 76 -- 88@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 76 -- 82@LB@
125	0.02168	0.5385	b3380	yhfW	-9.99	0.106098	159 -- 190	48 -- 81	phosphopentomutase-related metalloenzyme superfamily protein	_____________158_________________________________191\n_____________\|___________________________________\|\n5'-CUC...GAAAU___C___C________GAC___CUU__________UGGGG...GUG-3'\n______________CGU_GGU____GUUAU___AGU___GGAAACUCUC\n______________\|\|\|_\|\|:____\|\|\|\|\|___\|\|\|___:\|\|\|\|\|\|\|\|\|\n______________GCA_CCG____CAAUA___UCA___UCUUUGAGAG\n3'-CGC...CAAGU___A___AAAU_____AGC___AC___________CUUUG...AAG-5'\n_____________\|___________________________________\|\n_____________82__________________________________47\n	184 -- 190	48 -- 54	-22.1995 kcal/mol	7.79728 kcal/mol	4.41067 kcal/mol	158 191@LB@ \| \|@LB@5'-CUC...GAAAU C C GAC CUU UGGGG...GUG-3'@LB@ CGU GGU GUUAU AGU GGAAACUCUC@LB@ \|\|\| \|\|: \|\|\|\|\| \|\|\| :\|\|\|\|\|\|\|\|\|@LB@ GCA CCG CAAUA UCA UCUUUGAGAG@LB@3'-CGC...CAAGU A AAAU AGC AC CUUUG...AAG-5'@LB@ \| \|@LB@ 82 47@LB@@LB@@LB@Energy -9.99 kcal/mol@LB@Hybridization Energy -22.1995 kcal/mol@LB@Unfolding Energy - mRNA 7.79728 kcal/mol@LB@Unfolding Energy - sRNA 4.41067 kcal/mol@LB@@LB@Position - mRNA 159 -- 190@LB@Position - sRNA 48 -- 81@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 48 -- 54@LB@
174	0.03067	0.5559	b4005	purD	-11.17	0.066076	4 -- 22	73 -- 90	phosphoribosylglycinamide synthetase phosphoribosylamine-glycine ligase	_____________3___________________23\n_____________\|___________________\|\n________5'-GUG________CU__A______CUGAC...GUA-3'\n______________AAAGGUUC__CG_UGGCUU\n______________\|\|\|:\|\|\|\|__\|\|_\|\|\|\|\|\|\n______________UUUUCAAG__GC_ACCGAA\n3'-CGC...AGGCG________U___A______AUCAA...AAG-5'\n_____________\|___________________\|\n_____________91__________________72\n	5 -- 11	83 -- 89	-16.9563 kcal/mol	5.26463 kcal/mol	0.517799 kcal/mol	3 23@LB@ \| \|@LB@ 5'-GUG CU A CUGAC...GUA-3'@LB@ AAAGGUUC CG UGGCUU@LB@ \|\|\|:\|\|\|\| \|\| \|\|\|\|\|\|@LB@ UUUUCAAG GC ACCGAA@LB@3'-CGC...AGGCG U A AUCAA...AAG-5'@LB@ \| \|@LB@ 91 72@LB@@LB@@LB@Energy -11.17 kcal/mol@LB@Hybridization Energy -16.9563 kcal/mol@LB@Unfolding Energy - mRNA 5.26463 kcal/mol@LB@Unfolding Energy - sRNA 0.517799 kcal/mol@LB@@LB@Position - mRNA 4 -- 22@LB@Position - sRNA 73 -- 90@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 83 -- 89@LB@
110	0.0189	0.5385	b3175	secG	-9.72	0.118042	86 -- 106	67 -- 90	preprotein translocase membrane subunit	_____________85_______________________107\n_____________\|________________________\|\n5'-GCG...CUUGC__________UC____________GUAUU...CCU-3'\n______________GAAGG_UCAU____GCUUUGGUUA\n______________:\|\|:\|_\|\|\|:____\|\|\|\|\|:\|\|\|\|\n______________UUUUC_AGUG____CGAAAUCAAU\n3'-CGC...AGGCG_____A____CAAC__________AAGCU...AAG-5'\n_____________\|________________________\|\n_____________91_______________________66\n	100 -- 106	67 -- 73	-15.607 kcal/mol	5.31183 kcal/mol	0.573552 kcal/mol	85 107@LB@ \| \|@LB@5'-GCG...CUUGC UC GUAUU...CCU-3'@LB@ GAAGG UCAU GCUUUGGUUA@LB@ :\|\|:\| \|\|\|: \|\|\|\|\|:\|\|\|\|@LB@ UUUUC AGUG CGAAAUCAAU@LB@3'-CGC...AGGCG A CAAC AAGCU...AAG-5'@LB@ \| \|@LB@ 91 66@LB@@LB@@LB@Energy -9.72 kcal/mol@LB@Hybridization Energy -15.607 kcal/mol@LB@Unfolding Energy - mRNA 5.31183 kcal/mol@LB@Unfolding Energy - sRNA 0.573552 kcal/mol@LB@@LB@Position - mRNA 86 -- 106@LB@Position - sRNA 67 -- 90@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 67 -- 73@LB@
62	0.01254	0.5385	b0027	lspA	-10.68	0.080768	51 -- 66	75 -- 90	prolipoprotein signal peptidase (signal peptidase II)	_____________50________________67\n_____________\|_________________\|\n5'-UAU...GGGCU______________A__AAAGC...ACU-3'\n______________GAAAG_UCGCGUUG_GU\n______________:\|\|\|\|_\|\|:\|\|\|\|\|_\|:\n______________UUUUC_AGUGCAAC_CG\n3'-CGC...AGGCG_____A___________AAAUC...AAG-5'\n_____________\|_________________\|\n_____________91________________74\n	57 -- 63	77 -- 83	-15.4073 kcal/mol	4.21469 kcal/mol	0.517251 kcal/mol	50 67@LB@ \| \|@LB@5'-UAU...GGGCU A AAAGC...ACU-3'@LB@ GAAAG UCGCGUUG GU@LB@ :\|\|\|\| \|\|:\|\|\|\|\| \|:@LB@ UUUUC AGUGCAAC CG@LB@3'-CGC...AGGCG A AAAUC...AAG-5'@LB@ \| \|@LB@ 91 74@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -15.4073 kcal/mol@LB@Unfolding Energy - mRNA 4.21469 kcal/mol@LB@Unfolding Energy - sRNA 0.517251 kcal/mol@LB@@LB@Position - mRNA 51 -- 66@LB@Position - sRNA 75 -- 90@LB@Position Seed - mRNA 57 -- 63@LB@Position Seed - sRNA 77 -- 83@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@
123	0.02095	0.5385	b2562	yfhL	-10.74	0.078719	174 -- 195	59 -- 77	putative 4Fe-4S cluster-containing protein	_____________173____________________196\n_____________\|______________________\|\n5'-AGC...CGCCC_____GU_______UGA_____UCCUU...UUA-3'\n______________GGUUU__GUUGUUU___GAGUU\n______________\|\|:\|\|__\|\|\|:\|\|:___\|\|\|\|\|\n______________CCGAA__CAAUAAG___CUCAA\n3'-CGC...UGCAA_____AU_______________CUCUU...AAG-5'\n_____________\|______________________\|\n_____________78_____________________58\n	181 -- 187	64 -- 70	-15.8972 kcal/mol	4.34594 kcal/mol	0.811926 kcal/mol	173 196@LB@ \| \|@LB@5'-AGC...CGCCC GU UGA UCCUU...UUA-3'@LB@ GGUUU GUUGUUU GAGUU@LB@ \|\|:\|\| \|\|\|:\|\|: \|\|\|\|\|@LB@ CCGAA CAAUAAG CUCAA@LB@3'-CGC...UGCAA AU CUCUU...AAG-5'@LB@ \| \|@LB@ 78 58@LB@@LB@@LB@Energy -10.74 kcal/mol@LB@Hybridization Energy -15.8972 kcal/mol@LB@Unfolding Energy - mRNA 4.34594 kcal/mol@LB@Unfolding Energy - sRNA 0.811926 kcal/mol@LB@@LB@Position - mRNA 174 -- 195@LB@Position - sRNA 59 -- 77@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 64 -- 70@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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