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
9	0.0016	0.5385	b1709	btuD	-9.25	0.141890	185 -- 194	75 -- 84	vitamin B12 ABC transporter ATPase	_____________184________195\n_____________\|__________\|\n5'-GCA...UAAAC_G________AAAAU...GGC-3'\n______________U_GCGUUGGC\n______________\|_:\|\|\|\|\|\|\|\n______________A_UGCAACCG\n3'-CGC...UUUCA_G________AAAUC...AAG-5'\n_____________\|__________\|\n_____________85_________74\n	188 -- 194	75 -- 81	-15.1998 kcal/mol	5.44246 kcal/mol	0.505918 kcal/mol	184 195@LB@ \| \|@LB@5'-GCA...UAAAC G AAAAU...GGC-3'@LB@ U GCGUUGGC@LB@ \| :\|\|\|\|\|\|\|@LB@ A UGCAACCG@LB@3'-CGC...UUUCA G AAAUC...AAG-5'@LB@ \| \|@LB@ 85 74@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -15.1998 kcal/mol@LB@Unfolding Energy - mRNA 5.44246 kcal/mol@LB@Unfolding Energy - sRNA 0.505918 kcal/mol@LB@@LB@Position - mRNA 185 -- 194@LB@Position - sRNA 75 -- 84@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 75 -- 81@LB@
10	0.001846	0.5385	b2099	yegU	-13.29	0.027829	185 -- 270	5 -- 83	ADP-ribosylglycohydrolase family protein	_____________184_________________________________________________________________________________________271\n_____________\|___________________________________________________________________________________________\|\n5'-GUG...GUUGA___AAG__GA_______AA___AAAC____CGU________U__UCUUUAU__________G_______A__C__U____A__________AGCUU...CAC-3'\n______________CAC___GG____AGUUA__UGA____AGAA___AUUCUCGG_GC_______GGGCAG__GC_UUAGGGG_UG_GA_GGGG_UGCC_CUCCG\n______________\|\|\|___\|\|____\|\|\|\|\|__:\|\|____\|\|\|\|___\|:\|\|\|\|\|:_:\|_______\|\|\|\|\|\|__:\|_\|:\|:\|\|\|_\|:_:\|_\|:\|\|_\|\|\|\|_\|\|\|\|\|\n______________GUG___CC____UCAAU__GCU____UCUU___UGAGAGCU_UG_______CCCGUC__UG_AGUUCCC_AU_UU_CUCC_ACGG_GAGGC\n3'-CGC...UUCAA___CAA__GAAA_____AA___CAAC_______________U_______________AC__A_______A__U____________C_____AAAG-5'\n_____________\|___________________________________________________________________________________________\|\n_____________84__________________________________________________________________________________________4\n	243 -- 249	25 -- 31	-60.0716 kcal/mol	25.1194 kcal/mol	21.6578 kcal/mol	184 271@LB@ \| \|@LB@5'-GUG...GUUGA AAG GA AA AAAC CGU U UCUUUAU G A C U A AGCUU...CAC-3'@LB@ CAC GG AGUUA UGA AGAA AUUCUCGG GC GGGCAG GC UUAGGGG UG GA GGGG UGCC CUCCG@LB@ \|\|\| \|\| \|\|\|\|\| :\|\| \|\|\|\| \|:\|\|\|\|\|: :\| \|\|\|\|\|\| :\| \|:\|:\|\|\| \|: :\| \|:\|\| \|\|\|\| \|\|\|\|\|@LB@ GUG CC UCAAU GCU UCUU UGAGAGCU UG CCCGUC UG AGUUCCC AU UU CUCC ACGG GAGGC@LB@3'-CGC...UUCAA CAA GAAA AA CAAC U AC A A U C AAAG-5'@LB@ \| \|@LB@ 84 4@LB@@LB@@LB@Energy -13.29 kcal/mol@LB@Hybridization Energy -60.0716 kcal/mol@LB@Unfolding Energy - mRNA 25.1194 kcal/mol@LB@Unfolding Energy - sRNA 21.6578 kcal/mol@LB@@LB@Position - mRNA 185 -- 270@LB@Position - sRNA 5 -- 83@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 25 -- 31@LB@
115	0.01932	0.5385	b3475	acpT	-9.48	0.130030	187 -- 194	75 -- 82	4'-phosphopantetheinyl transferase	_____________186______195\n_____________\|________\|\n5'-GGG...AUUAA________CCUGA...GCU-3'\n______________ACGUUGGC\n______________\|\|\|\|\|\|\|\|\n______________UGCAACCG\n3'-CGC...UCAAG________AAAUC...AAG-5'\n_____________\|________\|\n_____________83_______74\n	188 -- 194	75 -- 81	-13.2305 kcal/mol	3.41608 kcal/mol	0.339284 kcal/mol	186 195@LB@ \| \|@LB@5'-GGG...AUUAA CCUGA...GCU-3'@LB@ ACGUUGGC@LB@ \|\|\|\|\|\|\|\|@LB@ UGCAACCG@LB@3'-CGC...UCAAG AAAUC...AAG-5'@LB@ \| \|@LB@ 83 74@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -13.2305 kcal/mol@LB@Unfolding Energy - mRNA 3.41608 kcal/mol@LB@Unfolding Energy - sRNA 0.339284 kcal/mol@LB@@LB@Position - mRNA 187 -- 194@LB@Position - sRNA 75 -- 82@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 75 -- 81@LB@
178	0.03115	0.5559	b2528	iscA	-9.66	0.120899	187 -- 207	62 -- 80	FeS cluster assembly protein	_____________186___________________208\n_____________\|_____________________\|\n5'-UUC...UAAGA____A_G_________G____UUACA...CCG-3'\n______________GUUG_G_UUUGGUUAU_UCGA\n______________\|\|\|\|_\|_\|\|\|:\|\|\|\|\|_\|\|\|\|\n______________CAAC_C_AAAUCAAUA_AGCU\n3'-CGC...AAGUG______G______________CAACU...AAG-5'\n_____________\|_____________________\|\n_____________81____________________61\n	196 -- 202	66 -- 72	-17.7068 kcal/mol	7.30815 kcal/mol	0.737855 kcal/mol	186 208@LB@ \| \|@LB@5'-UUC...UAAGA A G G UUACA...CCG-3'@LB@ GUUG G UUUGGUUAU UCGA@LB@ \|\|\|\| \| \|\|\|:\|\|\|\|\| \|\|\|\|@LB@ CAAC C AAAUCAAUA AGCU@LB@3'-CGC...AAGUG G CAACU...AAG-5'@LB@ \| \|@LB@ 81 61@LB@@LB@@LB@Energy -9.66 kcal/mol@LB@Hybridization Energy -17.7068 kcal/mol@LB@Unfolding Energy - mRNA 7.30815 kcal/mol@LB@Unfolding Energy - sRNA 0.737855 kcal/mol@LB@@LB@Position - mRNA 187 -- 207@LB@Position - sRNA 62 -- 80@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 66 -- 72@LB@
78	0.01399	0.5385	b3526	kdgK	-7.99	0.228654	189 -- 197	80 -- 88	2-dehydro-3-deoxygluconokinase	_____________188_______198\n_____________\|_________\|\n5'-CCC...AGAUC_________ACUAU...CUU-3'\n______________AGGUUCACG\n______________\|:\|\|\|\|\|\|\|\n______________UUCAAGUGC\n3'-CGC...GCGUU_________AACCG...AAG-5'\n_____________\|_________\|\n_____________89________79\n	191 -- 197	80 -- 86	-11.7911 kcal/mol	3.29177 kcal/mol	0.504555 kcal/mol	188 198@LB@ \| \|@LB@5'-CCC...AGAUC ACUAU...CUU-3'@LB@ AGGUUCACG@LB@ \|:\|\|\|\|\|\|\|@LB@ UUCAAGUGC@LB@3'-CGC...GCGUU AACCG...AAG-5'@LB@ \| \|@LB@ 89 79@LB@@LB@@LB@Energy -7.99 kcal/mol@LB@Hybridization Energy -11.7911 kcal/mol@LB@Unfolding Energy - mRNA 3.29177 kcal/mol@LB@Unfolding Energy - sRNA 0.504555 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 80 -- 88@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 80 -- 86@LB@
82	0.01477	0.5385	b3527	yhjJ	-9.01	0.155560	190 -- 221	62 -- 91	putative periplasmic M16 family chaperone	_____________189_______________________________222\n_____________\|_________________________________\|\n5'-CUC...UUGAU___________AUGCAG___ACAAAA_______CUUUU...GGC-3'\n______________CAGGGGUUCAC______GGC_______AUUCGA\n______________\|\|:::\|\|\|\|\|\|______\|\|\|_______\|\|\|\|\|\|\n______________GUUUUCAAGUG______CCG_______UAAGCU\n3'-CGC...UAGGC___________CAA______AAAUCAA______CAACU...AAG-5'\n_____________\|_________________________________\|\n_____________92________________________________61\n	194 -- 200	81 -- 87	-19.9715 kcal/mol	6.94165 kcal/mol	4.01597 kcal/mol	189 222@LB@ \| \|@LB@5'-CUC...UUGAU AUGCAG ACAAAA CUUUU...GGC-3'@LB@ CAGGGGUUCAC GGC AUUCGA@LB@ \|\|:::\|\|\|\|\|\| \|\|\| \|\|\|\|\|\|@LB@ GUUUUCAAGUG CCG UAAGCU@LB@3'-CGC...UAGGC CAA AAAUCAA CAACU...AAG-5'@LB@ \| \|@LB@ 92 61@LB@@LB@@LB@Energy -9.01 kcal/mol@LB@Hybridization Energy -19.9715 kcal/mol@LB@Unfolding Energy - mRNA 6.94165 kcal/mol@LB@Unfolding Energy - sRNA 4.01597 kcal/mol@LB@@LB@Position - mRNA 190 -- 221@LB@Position - sRNA 62 -- 91@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 81 -- 87@LB@
24	0.00428	0.5385	b0090	murG	-10.85	0.075280	191 -- 203	77 -- 89	N-acetylglucosaminyl transferase	_____________190___________204\n_____________\|_____________\|\n5'-AUU...UGUAC__________A__AGUGG...GUU-3'\n______________GAGGUUCACG_UG\n______________:\|:\|\|\|\|\|\|\|_\|\|\n______________UUUCAAGUGC_AC\n3'-CGC...GGCGU__________A__CGAAA...AAG-5'\n_____________\|_____________\|\n_____________90____________76\n	194 -- 200	80 -- 86	-14.5499 kcal/mol	3.18923 kcal/mol	0.510111 kcal/mol	190 204@LB@ \| \|@LB@5'-AUU...UGUAC A AGUGG...GUU-3'@LB@ GAGGUUCACG UG@LB@ :\|:\|\|\|\|\|\|\| \|\|@LB@ UUUCAAGUGC AC@LB@3'-CGC...GGCGU A CGAAA...AAG-5'@LB@ \| \|@LB@ 90 76@LB@@LB@@LB@Energy -10.85 kcal/mol@LB@Hybridization Energy -14.5499 kcal/mol@LB@Unfolding Energy - mRNA 3.18923 kcal/mol@LB@Unfolding Energy - sRNA 0.510111 kcal/mol@LB@@LB@Position - mRNA 191 -- 203@LB@Position - sRNA 77 -- 89@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 80 -- 86@LB@
111	0.01894	0.5385	b2600	tyrA	-7.88	0.238290	191 -- 206	74 -- 89	fused chorismate mutase T/prephenate dehydrogenase	_____________190______________207\n_____________\|________________\|\n5'-UCG...CUUAA_________UA_____GCUGA...UGG-3'\n______________GAGGUUUAU__UGGUU\n______________:\|:\|\|\|:\|:__\|\|\|:\|\n______________UUUCAAGUG__ACCGA\n3'-CGC...GGCGU_________CA_____AAUCA...AAG-5'\n_____________\|________________\|\n_____________90_______________73\n	193 -- 199	81 -- 87	-12.4695 kcal/mol	4.06959 kcal/mol	0.517373 kcal/mol	190 207@LB@ \| \|@LB@5'-UCG...CUUAA UA GCUGA...UGG-3'@LB@ GAGGUUUAU UGGUU@LB@ :\|:\|\|\|:\|: \|\|\|:\|@LB@ UUUCAAGUG ACCGA@LB@3'-CGC...GGCGU CA AAUCA...AAG-5'@LB@ \| \|@LB@ 90 73@LB@@LB@@LB@Energy -7.88 kcal/mol@LB@Hybridization Energy -12.4695 kcal/mol@LB@Unfolding Energy - mRNA 4.06959 kcal/mol@LB@Unfolding Energy - sRNA 0.517373 kcal/mol@LB@@LB@Position - mRNA 191 -- 206@LB@Position - sRNA 74 -- 89@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 81 -- 87@LB@
103	0.01739	0.5385	b0945	pyrD	-8.62	0.180746	193 -- 204	79 -- 90	dihydro-orotate oxidase FMN-linked	_____________192__________205\n_____________\|____________\|\n5'-UGU...UCCAG____________ACUAC...CGU-3'\n______________GAGAGUUCAUGU\n______________:\|:\|\|\|\|\|\|:\|\|\n______________UUUUCAAGUGCA\n3'-CGC...AGGCG____________ACCGA...AAG-5'\n_____________\|____________\|\n_____________91___________78\n	198 -- 204	79 -- 85	-13.8118 kcal/mol	4.6828 kcal/mol	0.506924 kcal/mol	192 205@LB@ \| \|@LB@5'-UGU...UCCAG ACUAC...CGU-3'@LB@ GAGAGUUCAUGU@LB@ :\|:\|\|\|\|\|\|:\|\|@LB@ UUUUCAAGUGCA@LB@3'-CGC...AGGCG ACCGA...AAG-5'@LB@ \| \|@LB@ 91 78@LB@@LB@@LB@Energy -8.62 kcal/mol@LB@Hybridization Energy -13.8118 kcal/mol@LB@Unfolding Energy - mRNA 4.6828 kcal/mol@LB@Unfolding Energy - sRNA 0.506924 kcal/mol@LB@@LB@Position - mRNA 193 -- 204@LB@Position - sRNA 79 -- 90@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 79 -- 85@LB@
151	0.02561	0.5485	b4041	plsB	-9.39	0.134646	197 -- 210	74 -- 86	glycerol-3-phosphate O-acyltransferase	_____________196____________211\n_____________\|______________\|\n5'-UCG...ACAUC________CC____GGCCA...UGG-3'\n______________GUUUAUGU__GGCU\n______________\|\|\|:\|:\|\|__\|\|\|\|\n______________CAAGUGCA__CCGA\n3'-CGC...GUUUU________A_____AAUCA...AAG-5'\n_____________\|______________\|\n_____________87_____________73\n	198 -- 204	79 -- 85	-13.0466 kcal/mol	3.14742 kcal/mol	0.513318 kcal/mol	196 211@LB@ \| \|@LB@5'-UCG...ACAUC CC GGCCA...UGG-3'@LB@ GUUUAUGU GGCU@LB@ \|\|\|:\|:\|\| \|\|\|\|@LB@ CAAGUGCA CCGA@LB@3'-CGC...GUUUU A AAUCA...AAG-5'@LB@ \| \|@LB@ 87 73@LB@@LB@@LB@Energy -9.39 kcal/mol@LB@Hybridization Energy -13.0466 kcal/mol@LB@Unfolding Energy - mRNA 3.14742 kcal/mol@LB@Unfolding Energy - sRNA 0.513318 kcal/mol@LB@@LB@Position - mRNA 197 -- 210@LB@Position - sRNA 74 -- 86@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 79 -- 85@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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