Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
21	0.000535	0.08206	b1639	mliC	-10.27	0.013452	27 -- 40	8 -- 21	inhibitor of c-type lysozyme membrane-bound; putative lipoprotein	_____________26_____________41\n_____________\|______________\|\n5'-GCU...GGGAU______________CCUUC...UGG-3'\n______________UACCAGGAAAUCUG\n______________:\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________GUGGUCCUUUAGAC\n3'-UUU...GCAAU______________UACACAA-5'\n_____________\|______________\|\n_____________22_____________7\n	32 -- 38	10 -- 16	-22.0821 kcal/mol	4.25106 kcal/mol	7.55865 kcal/mol	26 41@LB@ \| \|@LB@5'-GCU...GGGAU CCUUC...UGG-3'@LB@ UACCAGGAAAUCUG@LB@ :\|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ GUGGUCCUUUAGAC@LB@3'-UUU...GCAAU UACACAA-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -10.27 kcal/mol@LB@Hybridization Energy -22.0821 kcal/mol@LB@Unfolding Energy - mRNA 4.25106 kcal/mol@LB@Unfolding Energy - sRNA 7.55865 kcal/mol@LB@@LB@Position - mRNA 27 -- 40@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 10 -- 16@LB@
22	0.0006536	0.09021	b1245	oppC	-8.46	0.045181	270 -- 288	37 -- 58	oligopeptide ABC transporter permease	_____________269____________________289\n_____________\|______________________\|\n5'-GGU...GGCGC_________________C____GUCGA...UUA-3'\n______________AGCUUGU___GGCAGGA_GCAC\n______________\|:\|\|\|\|:___:\|\|\|:\|\|_\|\|\|\|\n______________UUGAACG___UCGUUCU_CGUG\n3'-UUU...CUACU_______AAU_______U____AAUUU...CAA-5'\n_____________\|______________________\|\n_____________59_____________________36\n	277 -- 283	42 -- 48	-22.602 kcal/mol	7.90039 kcal/mol	6.24354 kcal/mol	269 289@LB@ \| \|@LB@5'-GGU...GGCGC C GUCGA...UUA-3'@LB@ AGCUUGU GGCAGGA GCAC@LB@ \|:\|\|\|\|: :\|\|\|:\|\| \|\|\|\|@LB@ UUGAACG UCGUUCU CGUG@LB@3'-UUU...CUACU AAU U AAUUU...CAA-5'@LB@ \| \|@LB@ 59 36@LB@@LB@@LB@Energy -8.46 kcal/mol@LB@Hybridization Energy -22.602 kcal/mol@LB@Unfolding Energy - mRNA 7.90039 kcal/mol@LB@Unfolding Energy - sRNA 6.24354 kcal/mol@LB@@LB@Position - mRNA 270 -- 288@LB@Position - sRNA 37 -- 58@LB@Position Seed - mRNA 277 -- 283@LB@Position Seed - sRNA 42 -- 48@LB@
23	0.000685	0.09021	b3780	rhlB	-7.99	0.060609	254 -- 278	29 -- 60	ATP-dependent RNA helicase	_____________253______________________________279\n_____________\|________________________________\|\n5'-UCG...CAUCC____G_________________C_________AAAGG...CGC-3'\n______________GAAG_UUGU_______AGAAGC_CUUGAAAAA\n______________\|\|\|:_\|\|\|:_______\|\|\|\|\|\|_\|\|\|:\|\|\|\|\|\n______________CUUU_AACG_______UCUUCG_GAAUUUUUU\n3'-UUU...CCCUA____G____AAUUCGU______U_________AAGCA...CAA-5'\n_____________\|________________________________\|\n_____________61_______________________________28\n	270 -- 276	31 -- 37	-19.7636 kcal/mol	5.50064 kcal/mol	6.27092 kcal/mol	253 279@LB@ \| \|@LB@5'-UCG...CAUCC G C AAAGG...CGC-3'@LB@ GAAG UUGU AGAAGC CUUGAAAAA@LB@ \|\|\|: \|\|\|: \|\|\|\|\|\| \|\|\|:\|\|\|\|\|@LB@ CUUU AACG UCUUCG GAAUUUUUU@LB@3'-UUU...CCCUA G AAUUCGU U AAGCA...CAA-5'@LB@ \| \|@LB@ 61 28@LB@@LB@@LB@Energy -7.99 kcal/mol@LB@Hybridization Energy -19.7636 kcal/mol@LB@Unfolding Energy - mRNA 5.50064 kcal/mol@LB@Unfolding Energy - sRNA 6.27092 kcal/mol@LB@@LB@Position - mRNA 254 -- 278@LB@Position - sRNA 29 -- 60@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 31 -- 37@LB@
24	0.000694	0.09021	b2531	iscR	-7.21	0.097486	53 -- 65	27 -- 41	isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress- and iron starvation-inducible; autorepressor	_____________52______________66\n_____________\|_______________\|\n5'-AUG...AAAAU_______________AAAUA...AAC-3'\n______________GGCACU__GAAGGUU\n______________:\|\|\|\|\|__:\|\|::\|\|\n______________UCGUGA__UUUUUAA\n3'-UUU...GUUCU______AU_______GCAAU...CAA-5'\n_____________\|_______________\|\n_____________42______________26\n	59 -- 65	27 -- 33	-10.1429 kcal/mol	1.29 kcal/mol	1.6427 kcal/mol	52 66@LB@ \| \|@LB@5'-AUG...AAAAU AAAUA...AAC-3'@LB@ GGCACU GAAGGUU@LB@ :\|\|\|\|\| :\|\|::\|\|@LB@ UCGUGA UUUUUAA@LB@3'-UUU...GUUCU AU GCAAU...CAA-5'@LB@ \| \|@LB@ 42 26@LB@@LB@@LB@Energy -7.21 kcal/mol@LB@Hybridization Energy -10.1429 kcal/mol@LB@Unfolding Energy - mRNA 1.29 kcal/mol@LB@Unfolding Energy - sRNA 1.6427 kcal/mol@LB@@LB@Position - mRNA 53 -- 65@LB@Position - sRNA 27 -- 41@LB@Position Seed - mRNA 59 -- 65@LB@Position Seed - sRNA 27 -- 33@LB@
25	0.0007384	0.09021	b3434	yhgN	-11.94	0.004015	159 -- 197	7 -- 41	UPF0056 family inner membrane protein	_____________158_____________________________________198\n_____________\|_______________________________________\|\n5'-UUU...UUGUU_____GC_______CCG__GCAAU_______________GUUAU...CGA-3'\n______________AGCAC__AGAAAGU___CG_____UAUCAGGGAAUUUGA\n______________\|\|\|\|\|__\|:\|\|\|:\|___\|\|_____:\|:\|\|\|\|:\|\|\|:\|\|\|\n______________UCGUG__UUUUUUA___GC_____GUGGUCCUUUAGACU\n3'-UUU...GUUCU_____AA_______A____AAU_________________ACACAA-5'\n_____________\|_______________________________________\|\n_____________42______________________________________6\n	188 -- 194	10 -- 16	-30.001 kcal/mol	8.83552 kcal/mol	9.22092 kcal/mol	158 198@LB@ \| \|@LB@5'-UUU...UUGUU GC CCG GCAAU GUUAU...CGA-3'@LB@ AGCAC AGAAAGU CG UAUCAGGGAAUUUGA@LB@ \|\|\|\|\| \|:\|\|\|:\| \|\| :\|:\|\|\|\|:\|\|\|:\|\|\|@LB@ UCGUG UUUUUUA GC GUGGUCCUUUAGACU@LB@3'-UUU...GUUCU AA A AAU ACACAA-5'@LB@ \| \|@LB@ 42 6@LB@@LB@@LB@Energy -11.94 kcal/mol@LB@Hybridization Energy -30.001 kcal/mol@LB@Unfolding Energy - mRNA 8.83552 kcal/mol@LB@Unfolding Energy - sRNA 9.22092 kcal/mol@LB@@LB@Position - mRNA 159 -- 197@LB@Position - sRNA 7 -- 41@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 10 -- 16@LB@
26	0.0007705	0.09021	b3991	thiG	-9.33	0.025562	246 -- 261	25 -- 41	thiamine biosynthesis ThiGH complex subunit	_____________245_______________262\n_____________\|_________________\|\n5'-GCA...UUACC_____A___________CUUCU...CCG-3'\n______________GGCAC__GGGAAAUUCG\n______________:\|\|\|\|__:::\|\|\|\|\|\|\|\n______________UCGUG__UUUUUUAAGC\n3'-UUU...GUUCU_____AA__________AAUGU...CAA-5'\n_____________\|_________________\|\n_____________42________________24\n	255 -- 261	25 -- 31	-14.087 kcal/mol	3.10801 kcal/mol	1.64839 kcal/mol	245 262@LB@ \| \|@LB@5'-GCA...UUACC A CUUCU...CCG-3'@LB@ GGCAC GGGAAAUUCG@LB@ :\|\|\|\| :::\|\|\|\|\|\|\|@LB@ UCGUG UUUUUUAAGC@LB@3'-UUU...GUUCU AA AAUGU...CAA-5'@LB@ \| \|@LB@ 42 24@LB@@LB@@LB@Energy -9.33 kcal/mol@LB@Hybridization Energy -14.087 kcal/mol@LB@Unfolding Energy - mRNA 3.10801 kcal/mol@LB@Unfolding Energy - sRNA 1.64839 kcal/mol@LB@@LB@Position - mRNA 246 -- 261@LB@Position - sRNA 25 -- 41@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 25 -- 31@LB@
27	0.0008083	0.09021	b2711	norW	-10.17	0.014477	99 -- 112	13 -- 26	NADH:flavorubredoxin oxidoreductase	_____________98_____________113\n_____________\|______________\|\n5'-GAA...CAGGA______________CGCCG...UUG-3'\n______________CGUUGCGCCAGGAA\n______________\|\|\|\|:\|:\|\|\|\|\|\|\|\n______________GCAAUGUGGUCCUU\n3'-UUU...UUUAA______________UAGAC...CAA-5'\n_____________\|______________\|\n_____________27_____________12\n	106 -- 112	13 -- 19	-23.5838 kcal/mol	5.14562 kcal/mol	8.27144 kcal/mol	98 113@LB@ \| \|@LB@5'-GAA...CAGGA CGCCG...UUG-3'@LB@ CGUUGCGCCAGGAA@LB@ \|\|\|\|:\|:\|\|\|\|\|\|\|@LB@ GCAAUGUGGUCCUU@LB@3'-UUU...UUUAA UAGAC...CAA-5'@LB@ \| \|@LB@ 27 12@LB@@LB@@LB@Energy -10.17 kcal/mol@LB@Hybridization Energy -23.5838 kcal/mol@LB@Unfolding Energy - mRNA 5.14562 kcal/mol@LB@Unfolding Energy - sRNA 8.27144 kcal/mol@LB@@LB@Position - mRNA 99 -- 112@LB@Position - sRNA 13 -- 26@LB@Position Seed - mRNA 106 -- 112@LB@Position Seed - sRNA 13 -- 19@LB@
28	0.0008326	0.09021	b2563	acpS	-7.40	0.086911	170 -- 193	37 -- 61	holo-[acyl-carrier-protein] synthase 1	_____________169_______________________194\n_____________\|_________________________\|\n5'-GCC...AGAAA______GU___GAU__U________GUGGC...GCG-3'\n______________UGAAGC___CU___GC_GGAAGCGC\n______________\|\|\|\|:\|___\|\|___\|\|_:\|\|\|\|\|:\|\n______________ACUUUG___GA___CG_UCUUCGUG\n3'-UUU...GCCCU______AAC__AUU__U________AAUUU...CAA-5'\n_____________\|_________________________\|\n_____________62________________________36\n	187 -- 193	37 -- 43	-21.5547 kcal/mol	6.80255 kcal/mol	7.3495 kcal/mol	169 194@LB@ \| \|@LB@5'-GCC...AGAAA GU GAU U GUGGC...GCG-3'@LB@ UGAAGC CU GC GGAAGCGC@LB@ \|\|\|\|:\| \|\| \|\| :\|\|\|\|\|:\|@LB@ ACUUUG GA CG UCUUCGUG@LB@3'-UUU...GCCCU AAC AUU U AAUUU...CAA-5'@LB@ \| \|@LB@ 62 36@LB@@LB@@LB@Energy -7.40 kcal/mol@LB@Hybridization Energy -21.5547 kcal/mol@LB@Unfolding Energy - mRNA 6.80255 kcal/mol@LB@Unfolding Energy - sRNA 7.3495 kcal/mol@LB@@LB@Position - mRNA 170 -- 193@LB@Position - sRNA 37 -- 61@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 37 -- 43@LB@
29	0.000834	0.09021	b2798	ygdG	-11.41	0.005967	211 -- 245	24 -- 57	Ssb-binding protein misidentified as ExoIX	_____________210_________________________________246\n_____________\|___________________________________\|\n5'-CCA...UGUUC_________UUGUC__U_____GAAUCUU______CGCAU...UCG-3'\n______________AUUUGCUUA_____GA_GCACU_______AUUCGU\n______________\|:\|\|\|\|\|\|\|_____\|\|_\|\|\|\|\|_______\|\|\|\|\|\|\n______________UGAACGAAU_____CU_CGUGA_______UAAGCA\n3'-UUU...UACUU_________UCGUU__U_____AUUUUU_______AUGUG...CAA-5'\n_____________\|___________________________________\|\n_____________58__________________________________23\n	213 -- 219	49 -- 55	-23.2646 kcal/mol	5.57825 kcal/mol	6.27607 kcal/mol	210 246@LB@ \| \|@LB@5'-CCA...UGUUC UUGUC U GAAUCUU CGCAU...UCG-3'@LB@ AUUUGCUUA GA GCACU AUUCGU@LB@ \|:\|\|\|\|\|\|\| \|\| \|\|\|\|\| \|\|\|\|\|\|@LB@ UGAACGAAU CU CGUGA UAAGCA@LB@3'-UUU...UACUU UCGUU U AUUUUU AUGUG...CAA-5'@LB@ \| \|@LB@ 58 23@LB@@LB@@LB@Energy -11.41 kcal/mol@LB@Hybridization Energy -23.2646 kcal/mol@LB@Unfolding Energy - mRNA 5.57825 kcal/mol@LB@Unfolding Energy - sRNA 6.27607 kcal/mol@LB@@LB@Position - mRNA 211 -- 245@LB@Position - sRNA 24 -- 57@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 49 -- 55@LB@
30	0.0008402	0.09021	b2792	yqcC	-12.92	0.001907	10 -- 25	38 -- 53	DUF446 family protein	_____________9________________26\n_____________\|________________\|\n5'-AUC...GGGUG__G_____________AUAGU...AAU-3'\n______________GU_UGAGCAGGAAGCA\n______________\|:_\|:\|\|\|\|:\|\|\|\|\|\|\n______________CG_AUUCGUUCUUCGU\n3'-UUU...UUGAA__A_____________GAAUU...CAA-5'\n_____________\|________________\|\n_____________54_______________37\n	19 -- 25	38 -- 44	-21.2799 kcal/mol	2.27149 kcal/mol	6.09301 kcal/mol	9 26@LB@ \| \|@LB@5'-AUC...GGGUG G AUAGU...AAU-3'@LB@ GU UGAGCAGGAAGCA@LB@ \|: \|:\|\|\|\|:\|\|\|\|\|\|@LB@ CG AUUCGUUCUUCGU@LB@3'-UUU...UUGAA A GAAUU...CAA-5'@LB@ \| \|@LB@ 54 37@LB@@LB@@LB@Energy -12.92 kcal/mol@LB@Hybridization Energy -21.2799 kcal/mol@LB@Unfolding Energy - mRNA 2.27149 kcal/mol@LB@Unfolding Energy - sRNA 6.09301 kcal/mol@LB@@LB@Position - mRNA 10 -- 25@LB@Position - sRNA 38 -- 53@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 38 -- 44@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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