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
129	0.02219	0.5385	b4034	malE	-15.67	0.010476	105 -- 137	9 -- 40	maltose transporter subunit	_____________104_______________________________138\n_____________\|_________________________________\|\n5'-AGG...GGGGC____G___AAG____AUG_________U_____AUAAA...UGG-3'\n______________GUAG_GGC___GAGG___GAAAGAGGU_GCCGU\n______________\|:\|\|_\|:\|___:\|\|\|___:\|\|\|\|\|\|\|\|_\|\|\|\|:\n______________CGUC_CUG___UUCC___UUUUCUCCA_CGGCG\n3'-CGC...UUGCC____A___AAG____CAA_______________AGGCAAAG-5'\n_____________\|_________________________________\|\n_____________41________________________________8\n	125 -- 131	14 -- 20	-33.6959 kcal/mol	8.2816 kcal/mol	9.74463 kcal/mol	104 138@LB@ \| \|@LB@5'-AGG...GGGGC G AAG AUG U AUAAA...UGG-3'@LB@ GUAG GGC GAGG GAAAGAGGU GCCGU@LB@ \|:\|\| \|:\| :\|\|\| :\|\|\|\|\|\|\|\| \|\|\|\|:@LB@ CGUC CUG UUCC UUUUCUCCA CGGCG@LB@3'-CGC...UUGCC A AAG CAA AGGCAAAG-5'@LB@ \| \|@LB@ 41 8@LB@@LB@@LB@Energy -15.67 kcal/mol@LB@Hybridization Energy -33.6959 kcal/mol@LB@Unfolding Energy - mRNA 8.2816 kcal/mol@LB@Unfolding Energy - sRNA 9.74463 kcal/mol@LB@@LB@Position - mRNA 105 -- 137@LB@Position - sRNA 9 -- 40@LB@Position Seed - mRNA 125 -- 131@LB@Position Seed - sRNA 14 -- 20@LB@
130	0.02238	0.5385	b4365	yjjQ	-17.31	0.005324	260 -- 274	14 -- 28	putative transcriptional regulator	_____________259_____________275\n_____________\|_______________\|\n5'-AGG...CAAGC_______________CAUGA...AUG-3'\n______________AGGGUUAAAAGAGGU\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________UCCCAAUUUUCUCCA\n3'-CGC...GAAGU_______________CGGCG...AAG-5'\n_____________\|_______________\|\n_____________29______________13\n	268 -- 274	14 -- 20	-23.2971 kcal/mol	2.73817 kcal/mol	3.24497 kcal/mol	259 275@LB@ \| \|@LB@5'-AGG...CAAGC CAUGA...AUG-3'@LB@ AGGGUUAAAAGAGGU@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ UCCCAAUUUUCUCCA@LB@3'-CGC...GAAGU CGGCG...AAG-5'@LB@ \| \|@LB@ 29 13@LB@@LB@@LB@Energy -17.31 kcal/mol@LB@Hybridization Energy -23.2971 kcal/mol@LB@Unfolding Energy - mRNA 2.73817 kcal/mol@LB@Unfolding Energy - sRNA 3.24497 kcal/mol@LB@@LB@Position - mRNA 260 -- 274@LB@Position - sRNA 14 -- 28@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 14 -- 20@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@
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@
133	0.02275	0.5385	b0177	bamA	-6.79	0.350358	265 -- 271	23 -- 29	BamABCDE complex OM biogenesis outer membrane pore-forming assembly factor	_____________264_____272\n_____________\|_______\|\n5'-CUG...UGCUG_______CGUAG...GCC-3'\n______________AAGGGUU\n______________\|\|\|\|\|\|\|\n______________UUCCCAA\n3'-CGC...UGAAG_______UUUUC...AAG-5'\n_____________\|_______\|\n_____________30______22\n	265 -- 271	23 -- 29	-7.93739 kcal/mol	1.09969 kcal/mol	0.0462613 kcal/mol	264 272@LB@ \| \|@LB@5'-CUG...UGCUG CGUAG...GCC-3'@LB@ AAGGGUU@LB@ \|\|\|\|\|\|\|@LB@ UUCCCAA@LB@3'-CGC...UGAAG UUUUC...AAG-5'@LB@ \| \|@LB@ 30 22@LB@@LB@@LB@Energy -6.79 kcal/mol@LB@Hybridization Energy -7.93739 kcal/mol@LB@Unfolding Energy - mRNA 1.09969 kcal/mol@LB@Unfolding Energy - sRNA 0.0462613 kcal/mol@LB@@LB@Position - mRNA 265 -- 271@LB@Position - sRNA 23 -- 29@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 23 -- 29@LB@
134	0.0229	0.5385	b3729	glmS	-8.05	0.223933	255 -- 266	79 -- 90	L-glutamine:D-fructose-6-phosphate aminotransferase	_____________254__________267\n_____________\|____________\|\n5'-CAG...UUCUU____________CGUCU...GUC-3'\n______________GAAGGUUUACGU\n______________:\|\|:\|\|\|:\|\|\|\|\n______________UUUUCAAGUGCA\n3'-CGC...AGGCG____________ACCGA...AAG-5'\n_____________\|____________\|\n_____________91___________78\n	260 -- 266	79 -- 85	-12.2414 kcal/mol	3.68327 kcal/mol	0.506924 kcal/mol	254 267@LB@ \| \|@LB@5'-CAG...UUCUU CGUCU...GUC-3'@LB@ GAAGGUUUACGU@LB@ :\|\|:\|\|\|:\|\|\|\|@LB@ UUUUCAAGUGCA@LB@3'-CGC...AGGCG ACCGA...AAG-5'@LB@ \| \|@LB@ 91 78@LB@@LB@@LB@Energy -8.05 kcal/mol@LB@Hybridization Energy -12.2414 kcal/mol@LB@Unfolding Energy - mRNA 3.68327 kcal/mol@LB@Unfolding Energy - sRNA 0.506924 kcal/mol@LB@@LB@Position - mRNA 255 -- 266@LB@Position - sRNA 79 -- 90@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 79 -- 85@LB@
136	0.02309	0.5385	b3223	nanE	-8.63	0.180292	34 -- 47	74 -- 86	putative N-acetylmannosamine-6-P epimerase	_____________33_____________48\n_____________\|______________\|\n5'-AUC...CUCGC_____G________GCGCC...AAA-3'\n______________GUUCA_CGUUGGUU\n______________\|\|\|\|\|_\|\|\|\|\|\|:\|\n______________CAAGU_GCAACCGA\n3'-CGC...GUUUU______________AAUCA...AAG-5'\n_____________\|______________\|\n_____________87_____________73\n	41 -- 47	74 -- 80	-15.9355 kcal/mol	6.79344 kcal/mol	0.513318 kcal/mol	33 48@LB@ \| \|@LB@5'-AUC...CUCGC G GCGCC...AAA-3'@LB@ GUUCA CGUUGGUU@LB@ \|\|\|\|\| \|\|\|\|\|\|:\|@LB@ CAAGU GCAACCGA@LB@3'-CGC...GUUUU AAUCA...AAG-5'@LB@ \| \|@LB@ 87 73@LB@@LB@@LB@Energy -8.63 kcal/mol@LB@Hybridization Energy -15.9355 kcal/mol@LB@Unfolding Energy - mRNA 6.79344 kcal/mol@LB@Unfolding Energy - sRNA 0.513318 kcal/mol@LB@@LB@Position - mRNA 34 -- 47@LB@Position - sRNA 74 -- 86@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 74 -- 80@LB@
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@
138	0.02324	0.5385	b1826	mgrB	-8.64	0.179438	205 -- 238	60 -- 90	regulatory peptide for PhoPQ feedback inhibition	_____________204__________________________________239\n_____________\|____________________________________\|\n5'-UAC...AGUGA___________A___G_CGUUC__________U___GUUGG...AAU-3'\n______________AAAAGUUU_CG_UGG_U_____UGGUUGU_CG_GGU\n______________\|\|\|\|\|\|\|:_\|\|_\|\|\|_\|_____\|:\|\|\|:\|_\|\|_:\|\|\n______________UUUUCAAG_GC_ACC_A_____AUCAAUA_GC_UCA\n3'-CGC...AGGCG________U__A___G_A___________A______ACUCU...AAG-5'\n_____________\|____________________________________\|\n_____________91___________________________________59\n	226 -- 232	66 -- 72	-16.3224 kcal/mol	5.97183 kcal/mol	1.70935 kcal/mol	204 239@LB@ \| \|@LB@5'-UAC...AGUGA A G CGUUC U GUUGG...AAU-3'@LB@ AAAAGUUU CG UGG U UGGUUGU CG GGU@LB@ \|\|\|\|\|\|\|: \|\| \|\|\| \| \|:\|\|\|:\| \|\| :\|\|@LB@ UUUUCAAG GC ACC A AUCAAUA GC UCA@LB@3'-CGC...AGGCG U A G A A ACUCU...AAG-5'@LB@ \| \|@LB@ 91 59@LB@@LB@@LB@Energy -8.64 kcal/mol@LB@Hybridization Energy -16.3224 kcal/mol@LB@Unfolding Energy - mRNA 5.97183 kcal/mol@LB@Unfolding Energy - sRNA 1.70935 kcal/mol@LB@@LB@Position - mRNA 205 -- 238@LB@Position - sRNA 60 -- 90@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 66 -- 72@LB@
139	0.02326	0.5385	b1651	gloA	-10.25	0.095619	225 -- 233	75 -- 83	glyoxalase I Ni-dependent	_____________224_______234\n_____________\|_________\|\n5'-UGG...UGCUG_________GAUUU...AAA-3'\n______________CGCGUUGGC\n______________\|:\|\|\|\|\|\|\|\n______________GUGCAACCG\n3'-CGC...UUCAA_________AAAUC...AAG-5'\n_____________\|_________\|\n_____________84________74\n	227 -- 233	75 -- 81	-16.4206 kcal/mol	5.67498 kcal/mol	0.492259 kcal/mol	224 234@LB@ \| \|@LB@5'-UGG...UGCUG GAUUU...AAA-3'@LB@ CGCGUUGGC@LB@ \|:\|\|\|\|\|\|\|@LB@ GUGCAACCG@LB@3'-CGC...UUCAA AAAUC...AAG-5'@LB@ \| \|@LB@ 84 74@LB@@LB@@LB@Energy -10.25 kcal/mol@LB@Hybridization Energy -16.4206 kcal/mol@LB@Unfolding Energy - mRNA 5.67498 kcal/mol@LB@Unfolding Energy - sRNA 0.492259 kcal/mol@LB@@LB@Position - mRNA 225 -- 233@LB@Position - sRNA 75 -- 83@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 75 -- 81@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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