Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
1	0	0	b2687	luxS	-86.29	0.000000	61 -- 132	1 -- 72	S-ribosylhomocysteine lyase	_____________60_______________________________________________________________________133\n_____________\|________________________________________________________________________\|\n5'-GAA...AAAGA________________________________________________________________________AUAUA...UCA-3'\n______________AAAAGGCCACUCGUGAGUGGCCAAAAUUUCAUCUCUGAAUUCAGGGAUGAUGAUAACAAAUGCGCGUCUUUC\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________UUUUCCGGUGAGCACUCACCGGUUUUAAAGUAGAGACUUAAGUCCCUACUACUAUUGUUUACGCGCAGAAAG\n___________3'-________________________________________________________________________-5'\n______________\|______________________________________________________________________\|\n______________72_____________________________________________________________________1\n	126 -- 132	1 -- 7	-138.099 kcal/mol	30.0464 kcal/mol	21.7639 kcal/mol	60 133@LB@ \| \|@LB@5'-GAA...AAAGA AUAUA...UCA-3'@LB@ AAAAGGCCACUCGUGAGUGGCCAAAAUUUCAUCUCUGAAUUCAGGGAUGAUGAUAACAAAUGCGCGUCUUUC@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ UUUUCCGGUGAGCACUCACCGGUUUUAAAGUAGAGACUUAAGUCCCUACUACUAUUGUUUACGCGCAGAAAG@LB@ 3'- -5'@LB@ \| \|@LB@ 72 1@LB@@LB@@LB@Energy -86.29 kcal/mol@LB@Hybridization Energy -138.099 kcal/mol@LB@Unfolding Energy - mRNA 30.0464 kcal/mol@LB@Unfolding Energy - sRNA 21.7639 kcal/mol@LB@@LB@Position - mRNA 61 -- 132@LB@Position - sRNA 1 -- 72@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 1 -- 7@LB@
4	4.059e-05	0.03436	b2748	ftsB	-19.92	0.001892	154 -- 190	1 -- 44	cell division protein	_____________153___________________________________________191\n_____________\|_____________________________________________\|\n5'-GGG...UAGAG_______C____G__U_____________________________AGGGG...AUG-3'\n______________UCGUCUU_GGAU_CA_GGGAUGAUGA_______UGC_CGUUUUUC\n______________\|\|:\|\|\|:_\|:\|\|_\|\|_\|\|\|\|\|\|\|\|\|\|_______\|\|\|_\|\|\|:\|\|\|\|\n______________AGUAGAG_CUUA_GU_CCCUACUACU_______ACG_GCAGAAAG\n3'-UUU...UUUAA_______A____A_____________AUUGUUU___C________-5'\n_____________\|____________________________________________\|\n_____________45___________________________________________1\n	184 -- 190	1 -- 7	-40.1368 kcal/mol	10.7611 kcal/mol	9.45578 kcal/mol	153 191@LB@ \| \|@LB@5'-GGG...UAGAG C G U AGGGG...AUG-3'@LB@ UCGUCUU GGAU CA GGGAUGAUGA UGC CGUUUUUC@LB@ \|\|:\|\|\|: \|:\|\| \|\| \|\|\|\|\|\|\|\|\|\| \|\|\| \|\|\|:\|\|\|\|@LB@ AGUAGAG CUUA GU CCCUACUACU ACG GCAGAAAG@LB@3'-UUU...UUUAA A A AUUGUUU C -5'@LB@ \| \|@LB@ 45 1@LB@@LB@@LB@Energy -19.92 kcal/mol@LB@Hybridization Energy -40.1368 kcal/mol@LB@Unfolding Energy - mRNA 10.7611 kcal/mol@LB@Unfolding Energy - sRNA 9.45578 kcal/mol@LB@@LB@Position - mRNA 154 -- 190@LB@Position - sRNA 1 -- 44@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 1 -- 7@LB@
7	9.926e-05	0.04801	b1113	ldtC	-15.69	0.011765	184 -- 223	1 -- 45	L D-transpeptidase linking Lpp to murein	_____________183___________________________________________224\n_____________\|_____________________________________________\|\n5'-CGU...UUAUA______A________UU________________A___________UCGCU...UGC-3'\n______________UUUAUU__UGGAUUU___GGUGAUGAU__CAAA__CGCGUUUUUC\n______________\|\|:\|\|:__\|\|:\|\|\|:___\|:\|\|\|\|\|\|\|__\|\|\|\|__\|\|\|\|\|:\|\|\|\|\n______________AAGUAG__ACUUAAG___CUACUACUA__GUUU__GCGCAGAAAG\n3'-UUU...UUUUA______AG_______UCC_________UU____AC__________-5'\n_____________\|____________________________________________\|\n_____________46___________________________________________1\n	217 -- 223	1 -- 7	-33.7876 kcal/mol	8.63912 kcal/mol	9.46113 kcal/mol	183 224@LB@ \| \|@LB@5'-CGU...UUAUA A UU A UCGCU...UGC-3'@LB@ UUUAUU UGGAUUU GGUGAUGAU CAAA CGCGUUUUUC@LB@ \|\|:\|\|: \|\|:\|\|\|: \|:\|\|\|\|\|\|\| \|\|\|\| \|\|\|\|\|:\|\|\|\|@LB@ AAGUAG ACUUAAG CUACUACUA GUUU GCGCAGAAAG@LB@3'-UUU...UUUUA AG UCC UU AC -5'@LB@ \| \|@LB@ 46 1@LB@@LB@@LB@Energy -15.69 kcal/mol@LB@Hybridization Energy -33.7876 kcal/mol@LB@Unfolding Energy - mRNA 8.63912 kcal/mol@LB@Unfolding Energy - sRNA 9.46113 kcal/mol@LB@@LB@Position - mRNA 184 -- 223@LB@Position - sRNA 1 -- 45@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 1 -- 7@LB@
8	0.000167	0.07068	b0814	ompX	-11.11	0.078421	202 -- 223	1 -- 22	outer membrane protein X	_____________201____________________224\n_____________\|______________________\|\n5'-CUG...GGUUA___AAAA__U___A________AGCAC...CAC-3'\n______________UGA____AA_UGC_UGUCUUUC\n______________\|\|\|____\|\|_\|\|\|_:\|\|\|\|\|\|\|\n______________ACU____UU_ACG_GCAGAAAG\n3'-UUU...CUACU___AUUG__U___C________-5'\n_____________\|_____________________\|\n_____________23____________________1\n	217 -- 223	1 -- 7	-15.5509 kcal/mol	3.18554 kcal/mol	1.25963 kcal/mol	201 224@LB@ \| \|@LB@5'-CUG...GGUUA AAAA U A AGCAC...CAC-3'@LB@ UGA AA UGC UGUCUUUC@LB@ \|\|\| \|\| \|\|\| :\|\|\|\|\|\|\|@LB@ ACU UU ACG GCAGAAAG@LB@3'-UUU...CUACU AUUG U C -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -11.11 kcal/mol@LB@Hybridization Energy -15.5509 kcal/mol@LB@Unfolding Energy - mRNA 3.18554 kcal/mol@LB@Unfolding Energy - sRNA 1.25963 kcal/mol@LB@@LB@Position - mRNA 202 -- 223@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 1 -- 7@LB@
18	0.00061	0.1147	b2126	yehU	-11.17	0.076396	235 -- 252	1 -- 18	inner membrane putative sensory kinase in two-component system with YehT	_____________234________________253\n_____________\|__________________\|\n5'-GUC...GCUUC__________________UAGUC...UAA-3'\n______________AGCAGAUGUGCGUUUUUU\n______________\|:\|\|:\|\|\|:\|\|\|\|:\|\|\|:\n______________UUGUUUACGCGCAGAAAG\n3'-UUU...UACUA__________________-5'\n_____________\|_________________\|\n_____________19________________1\n	246 -- 252	1 -- 7	-22.3117 kcal/mol	9.89973 kcal/mol	1.24077 kcal/mol	234 253@LB@ \| \|@LB@5'-GUC...GCUUC UAGUC...UAA-3'@LB@ AGCAGAUGUGCGUUUUUU@LB@ \|:\|\|:\|\|\|:\|\|\|\|:\|\|\|:@LB@ UUGUUUACGCGCAGAAAG@LB@3'-UUU...UACUA -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -11.17 kcal/mol@LB@Hybridization Energy -22.3117 kcal/mol@LB@Unfolding Energy - mRNA 9.89973 kcal/mol@LB@Unfolding Energy - sRNA 1.24077 kcal/mol@LB@@LB@Position - mRNA 235 -- 252@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 1 -- 7@LB@
20	0.0008552	0.1448	b4137	cutA	-9.23	0.162618	220 -- 236	1 -- 16	divalent-cation tolerance protein copper sensitivity	_____________219_______________237\n_____________\|_________________\|\n5'-CAA...AAGUU_____AC_______G__GUGGU...CGG-3'\n______________CGAAU__CGCGUCU_UC\n______________\|:\|\|\|__\|\|\|\|\|\|\|_\|\|\n______________GUUUA__GCGCAGA_AG\n3'-UUU...CUAUU_____C________A__-5'\n_____________\|________________\|\n_____________17_______________1\n	227 -- 233	4 -- 10	-14.9299 kcal/mol	4.46216 kcal/mol	1.23857 kcal/mol	219 237@LB@ \| \|@LB@5'-CAA...AAGUU AC G GUGGU...CGG-3'@LB@ CGAAU CGCGUCU UC@LB@ \|:\|\|\| \|\|\|\|\|\|\| \|\|@LB@ GUUUA GCGCAGA AG@LB@3'-UUU...CUAUU C A -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -9.23 kcal/mol@LB@Hybridization Energy -14.9299 kcal/mol@LB@Unfolding Energy - mRNA 4.46216 kcal/mol@LB@Unfolding Energy - sRNA 1.23857 kcal/mol@LB@@LB@Position - mRNA 220 -- 236@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 4 -- 10@LB@
22	0.001004	0.1545	b0583	entD	-18.10	0.004183	41 -- 63	1 -- 22	phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex	_____________40______________________64\n_____________\|_______________________\|\n5'-AUA...CAGAU__U____A___________G___AUGCC...UGC-3'\n______________UG_UGAC_AAGUGCGCGUC_UUC\n______________\|\|_\|:\|\|_\|\|:\|\|\|\|\|\|\|\|_\|\|\|\n______________AC_AUUG_UUUACGCGCAG_AAG\n3'-UUU...CUACU__U________________A___-5'\n_____________\|______________________\|\n_____________23_____________________1\n	53 -- 59	5 -- 11	-24.6004 kcal/mol	5.24265 kcal/mol	1.25963 kcal/mol	40 64@LB@ \| \|@LB@5'-AUA...CAGAU U A G AUGCC...UGC-3'@LB@ UG UGAC AAGUGCGCGUC UUC@LB@ \|\| \|:\|\| \|\|:\|\|\|\|\|\|\|\| \|\|\|@LB@ AC AUUG UUUACGCGCAG AAG@LB@3'-UUU...CUACU U A -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -18.10 kcal/mol@LB@Hybridization Energy -24.6004 kcal/mol@LB@Unfolding Energy - mRNA 5.24265 kcal/mol@LB@Unfolding Energy - sRNA 1.25963 kcal/mol@LB@@LB@Position - mRNA 41 -- 63@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 5 -- 11@LB@
25	0.001519	0.1943	b2817	amiC	-17.97	0.004427	110 -- 131	1 -- 21	N-acetylmuramoyl-L-alanine amidase	_____________109____________________132\n_____________\|______________________\|\n5'-AGU...UAUUA__________UA__________GCUAA...UCA-3'\n______________GAUGACAGAU__UGCGUCUUUC\n______________\|\|\|:\|\|\|:\|\|__:\|\|\|\|\|\|\|\|\|\n______________CUAUUGUUUA__GCGCAGAAAG\n3'-UUU...UACUA__________C___________-5'\n_____________\|_____________________\|\n_____________22____________________1\n	125 -- 131	1 -- 7	-25.6931 kcal/mol	6.46841 kcal/mol	1.25763 kcal/mol	109 132@LB@ \| \|@LB@5'-AGU...UAUUA UA GCUAA...UCA-3'@LB@ GAUGACAGAU UGCGUCUUUC@LB@ \|\|\|:\|\|\|:\|\| :\|\|\|\|\|\|\|\|\|@LB@ CUAUUGUUUA GCGCAGAAAG@LB@3'-UUU...UACUA C -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -17.97 kcal/mol@LB@Hybridization Energy -25.6931 kcal/mol@LB@Unfolding Energy - mRNA 6.46841 kcal/mol@LB@Unfolding Energy - sRNA 1.25763 kcal/mol@LB@@LB@Position - mRNA 110 -- 131@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 125 -- 131@LB@Position Seed - sRNA 1 -- 7@LB@
45	0.00309	0.2325	b0584	fepA	-13.78	0.026215	91 -- 106	1 -- 17	ferrienterobactin outer membrane transporter	_____________90________________107\n_____________\|_________________\|\n5'-GAA...CAACU___C_____________AGGAU...ACG-3'\n______________GCA__UGCGUGUCUUUC\n______________:\|\|__\|\|\|\|:\|\|\|\|\|\|\|\n______________UGU__ACGCGCAGAAAG\n3'-UUU...ACUAU___UU____________-5'\n_____________\|________________\|\n_____________18_______________1\n	100 -- 106	1 -- 7	-21.1338 kcal/mol	6.10916 kcal/mol	1.23994 kcal/mol	90 107@LB@ \| \|@LB@5'-GAA...CAACU C AGGAU...ACG-3'@LB@ GCA UGCGUGUCUUUC@LB@ :\|\| \|\|\|\|:\|\|\|\|\|\|\|@LB@ UGU ACGCGCAGAAAG@LB@3'-UUU...ACUAU UU -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -13.78 kcal/mol@LB@Hybridization Energy -21.1338 kcal/mol@LB@Unfolding Energy - mRNA 6.10916 kcal/mol@LB@Unfolding Energy - sRNA 1.23994 kcal/mol@LB@@LB@Position - mRNA 91 -- 106@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 1 -- 7@LB@
51	0.004574	0.3024	b3529	yhjK	-9.99	0.121635	195 -- 213	1 -- 18	cyclic-di-GMP phosphodiesterase	_____________194_________________214\n_____________\|___________________\|\n5'-AGC...GGGGA_____UU_______AAG__GCUCG...AUC-3'\n______________GACAA__UGCGCGU___UC\n______________:\|\|\|\|__\|\|\|\|\|\|\|___\|\|\n______________UUGUU__ACGCGCA___AG\n3'-UUU...UACUA_____U________GAA__-5'\n_____________\|__________________\|\n_____________19_________________1\n	202 -- 208	6 -- 12	-16.8324 kcal/mol	5.6017 kcal/mol	1.24077 kcal/mol	194 214@LB@ \| \|@LB@5'-AGC...GGGGA UU AAG GCUCG...AUC-3'@LB@ GACAA UGCGCGU UC@LB@ :\|\|\|\| \|\|\|\|\|\|\| \|\|@LB@ UUGUU ACGCGCA AG@LB@3'-UUU...UACUA U GAA -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -9.99 kcal/mol@LB@Hybridization Energy -16.8324 kcal/mol@LB@Unfolding Energy - mRNA 5.6017 kcal/mol@LB@Unfolding Energy - sRNA 1.24077 kcal/mol@LB@@LB@Position - mRNA 195 -- 213@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 202 -- 208@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)

Job resubmission

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service.

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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