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	Additional homologs
16	0.0003675	0.07398	b0566	envY	-6.67	0.133095	149 -- 159	37 -- 47	porin thermoregulatory transcriptional activator	b1499 b0564 b3515 b4116 b3516	_____________148_________160\n_____________\|___________\|\n5'-GGC...CUCAU___________AGAUC...ACU-3'\n______________GCAGGAAGCAU\n______________\|\|\|:\|\|\|\|\|\|:\n______________CGUUCUUCGUG\n3'-UUU...GAAUU___________AAUUU...CAA-5'\n_____________\|___________\|\n_____________48__________36\n	153 -- 159	37 -- 43	-16.6622 kcal/mol	4.74809 kcal/mol	5.23944 kcal/mol	148 160@LB@ \| \|@LB@5'-GGC...CUCAU AGAUC...ACU-3'@LB@ GCAGGAAGCAU@LB@ \|\|\|:\|\|\|\|\|\|:@LB@ CGUUCUUCGUG@LB@3'-UUU...GAAUU AAUUU...CAA-5'@LB@ \| \|@LB@ 48 36@LB@@LB@@LB@Energy -6.67 kcal/mol@LB@Hybridization Energy -16.6622 kcal/mol@LB@Unfolding Energy - mRNA 4.74809 kcal/mol@LB@Unfolding Energy - sRNA 5.23944 kcal/mol@LB@@LB@Position - mRNA 149 -- 159@LB@Position - sRNA 37 -- 47@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 37 -- 43@LB@
197	0.0237	0.3864	b4001	yjaH	-6.58	0.140477	149 -- 175	29 -- 57	DUF1481 family putative lipoprotein		_____________148____________________________176\n_____________\|______________________________\|\n5'-UGG...CCGGC________CU____________________CGCAG...AUA-3'\n______________AUUUGUUU__GGCA__AGGCACU_GAAAGA\n______________\|:\|\|\|:\|\|__:\|\|\|__\|:\|\|\|\|\|_:\|\|\|:\|\n______________UGAACGAA__UCGU__UUCGUGA_UUUUUU\n3'-UUU...UACUU________U_____UC_______A______AAGCA...CAA-5'\n_____________\|______________________________\|\n_____________58_____________________________28\n	163 -- 169	36 -- 42	-19.7163 kcal/mol	6.91297 kcal/mol	6.22375 kcal/mol	148 176@LB@ \| \|@LB@5'-UGG...CCGGC CU CGCAG...AUA-3'@LB@ AUUUGUUU GGCA AGGCACU GAAAGA@LB@ \|:\|\|\|:\|\| :\|\|\| \|:\|\|\|\|\| :\|\|\|:\|@LB@ UGAACGAA UCGU UUCGUGA UUUUUU@LB@3'-UUU...UACUU U UC A AAGCA...CAA-5'@LB@ \| \|@LB@ 58 28@LB@@LB@@LB@Energy -6.58 kcal/mol@LB@Hybridization Energy -19.7163 kcal/mol@LB@Unfolding Energy - mRNA 6.91297 kcal/mol@LB@Unfolding Energy - sRNA 6.22375 kcal/mol@LB@@LB@Position - mRNA 149 -- 175@LB@Position - sRNA 29 -- 57@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 36 -- 42@LB@
7	4.438e-05	0.02042	b0794	ybhF	-10.77	0.009494	150 -- 165	11 -- 26	putative ABC transporter ATPase		_____________149______________166\n_____________\|________________\|\n5'-UAC...UGAUG________________GCCAG...GUU-3'\n______________CGUUACGCCAGGGAAU\n______________\|\|\|\|\|\|:\|\|\|\|\|:\|\|\|\n______________GCAAUGUGGUCCUUUA\n3'-UUU...UUUAA________________GACUA...CAA-5'\n_____________\|________________\|\n_____________27_______________10\n	157 -- 163	13 -- 19	-25.1629 kcal/mol	6.0475 kcal/mol	8.34814 kcal/mol	149 166@LB@ \| \|@LB@5'-UAC...UGAUG GCCAG...GUU-3'@LB@ CGUUACGCCAGGGAAU@LB@ \|\|\|\|\|\|:\|\|\|\|\|:\|\|\|@LB@ GCAAUGUGGUCCUUUA@LB@3'-UUU...UUUAA GACUA...CAA-5'@LB@ \| \|@LB@ 27 10@LB@@LB@@LB@Energy -10.77 kcal/mol@LB@Hybridization Energy -25.1629 kcal/mol@LB@Unfolding Energy - mRNA 6.0475 kcal/mol@LB@Unfolding Energy - sRNA 8.34814 kcal/mol@LB@@LB@Position - mRNA 150 -- 165@LB@Position - sRNA 11 -- 26@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 13 -- 19@LB@
147	0.01475	0.3231	b0084	ftsI	-4.75	0.360226	157 -- 172	24 -- 39	transpeptidase involved in septal peptidoglycan synthesis; penicillin-binding protein 3		_____________156_______________173\n_____________\|_________________\|\n5'-GUU...UCCGU___A________A____AGUGC...UGG-3'\n______________CAC__AGAAAAU_UCGU\n______________\|\|\|__\|:\|\|\|\|\|_\|\|\|\|\n______________GUG__UUUUUUA_AGCA\n3'-UUU...UCUUC___AA____________AUGUG...CAA-5'\n_____________\|_________________\|\n_____________40________________23\n	161 -- 167	28 -- 34	-7.76704 kcal/mol	1.36905 kcal/mol	1.64726 kcal/mol	156 173@LB@ \| \|@LB@5'-GUU...UCCGU A A AGUGC...UGG-3'@LB@ CAC AGAAAAU UCGU@LB@ \|\|\| \|:\|\|\|\|\| \|\|\|\|@LB@ GUG UUUUUUA AGCA@LB@3'-UUU...UCUUC AA AUGUG...CAA-5'@LB@ \| \|@LB@ 40 23@LB@@LB@@LB@Energy -4.75 kcal/mol@LB@Hybridization Energy -7.76704 kcal/mol@LB@Unfolding Energy - mRNA 1.36905 kcal/mol@LB@Unfolding Energy - sRNA 1.64726 kcal/mol@LB@@LB@Position - mRNA 157 -- 172@LB@Position - sRNA 24 -- 39@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 28 -- 34@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@
36	0.001384	0.121	b2573	rpoE	-5.96	0.197133	163 -- 178	25 -- 41	RNA polymerase sigma E factor		_____________162_______________179\n_____________\|_________________\|\n5'-ACA...UCGAU_____GU__________GUUUG...UGG-3'\n______________AGCGC___GGAAAUUUG\n______________\|\|\|:\|___::\|\|\|\|\|:\|\n______________UCGUG___UUUUUAAGC\n3'-UUU...GUUCU_____AAU_________AAUGU...CAA-5'\n_____________\|_________________\|\n_____________42________________24\n	172 -- 178	25 -- 31	-12.5895 kcal/mol	4.97735 kcal/mol	1.64839 kcal/mol	162 179@LB@ \| \|@LB@5'-ACA...UCGAU GU GUUUG...UGG-3'@LB@ AGCGC GGAAAUUUG@LB@ \|\|\|:\| ::\|\|\|\|\|:\|@LB@ UCGUG UUUUUAAGC@LB@3'-UUU...GUUCU AAU AAUGU...CAA-5'@LB@ \| \|@LB@ 42 24@LB@@LB@@LB@Energy -5.96 kcal/mol@LB@Hybridization Energy -12.5895 kcal/mol@LB@Unfolding Energy - mRNA 4.97735 kcal/mol@LB@Unfolding Energy - sRNA 1.64839 kcal/mol@LB@@LB@Position - mRNA 163 -- 178@LB@Position - sRNA 25 -- 41@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 25 -- 31@LB@
180	0.02111	0.3768	b2753	iap	-4.77	0.357003	164 -- 179	25 -- 40	aminopeptidase in alkaline phosphatase isozyme conversion		_____________163______________180\n_____________\|________________\|\n5'-UAG...CUAUG___G_A__________CAUGG...CUA-3'\n______________GCG_U_AAAAAAUUUG\n______________\|\|:_\|_\|\|\|\|\|\|\|\|:\|\n______________CGU_A_UUUUUUAAGC\n3'-UUU...UUCUU___G_A__________AAUGU...CAA-5'\n_____________\|________________\|\n_____________41_______________24\n	170 -- 176	28 -- 34	-8.71545 kcal/mol	2.29678 kcal/mol	1.64821 kcal/mol	163 180@LB@ \| \|@LB@5'-UAG...CUAUG G A CAUGG...CUA-3'@LB@ GCG U AAAAAAUUUG@LB@ \|\|: \| \|\|\|\|\|\|\|\|:\|@LB@ CGU A UUUUUUAAGC@LB@3'-UUU...UUCUU G A AAUGU...CAA-5'@LB@ \| \|@LB@ 41 24@LB@@LB@@LB@Energy -4.77 kcal/mol@LB@Hybridization Energy -8.71545 kcal/mol@LB@Unfolding Energy - mRNA 2.29678 kcal/mol@LB@Unfolding Energy - sRNA 1.64821 kcal/mol@LB@@LB@Position - mRNA 164 -- 179@LB@Position - sRNA 25 -- 40@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 28 -- 34@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@
13	0.0002543	0.06302	b3583	sgbE	-8.82	0.035786	171 -- 191	39 -- 61	L-ribulose-5-phosphate 4-epimerase		_____________170_____________________192\n_____________\|_______________________\|\n5'-CAA...UGGAU__________GUAU_________UGGAU...ACG-3'\n______________UGAAGC__GC____GCAGGAGGC\n______________\|\|\|\|:\|__\|\|____\|\|\|:\|\|:\|\|\n______________ACUUUG__CG____CGUUCUUCG\n3'-UUU...GCCCU______AA__AAUU_________UGAAU...CAA-5'\n_____________\|_______________________\|\n_____________62______________________38\n	185 -- 191	39 -- 45	-21.2799 kcal/mol	5.20492 kcal/mol	7.25518 kcal/mol	170 192@LB@ \| \|@LB@5'-CAA...UGGAU GUAU UGGAU...ACG-3'@LB@ UGAAGC GC GCAGGAGGC@LB@ \|\|\|\|:\| \|\| \|\|\|:\|\|:\|\|@LB@ ACUUUG CG CGUUCUUCG@LB@3'-UUU...GCCCU AA AAUU UGAAU...CAA-5'@LB@ \| \|@LB@ 62 38@LB@@LB@@LB@Energy -8.82 kcal/mol@LB@Hybridization Energy -21.2799 kcal/mol@LB@Unfolding Energy - mRNA 5.20492 kcal/mol@LB@Unfolding Energy - sRNA 7.25518 kcal/mol@LB@@LB@Position - mRNA 171 -- 191@LB@Position - sRNA 39 -- 61@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 39 -- 45@LB@
43	0.001794	0.1344	b0631	ybeD	-7.18	0.099343	171 -- 193	16 -- 40	UPF0250 family protein		_____________170________________________194\n_____________\|__________________________\|\n5'-GCU...GAGUU__U______UUA______________AGCUG...AAG-3'\n______________GC_AUUUAA______CGUUACGCCGG\n______________\|\|_\|:\|\|\|\|______\|\|\|\|\|\|:\|\|:\|\n______________CG_UGAAUU______GCAAUGUGGUC\n3'-UUU...UUCUU_________UUUUAA___________CUUUA...CAA-5'\n_____________\|__________________________\|\n_____________41_________________________15\n	187 -- 193	16 -- 22	-19.4847 kcal/mol	3.10673 kcal/mol	9.1996 kcal/mol	170 194@LB@ \| \|@LB@5'-GCU...GAGUU U UUA AGCUG...AAG-3'@LB@ GC AUUUAA CGUUACGCCGG@LB@ \|\| \|:\|\|\|\| \|\|\|\|\|\|:\|\|:\|@LB@ CG UGAAUU GCAAUGUGGUC@LB@3'-UUU...UUCUU UUUUAA CUUUA...CAA-5'@LB@ \| \|@LB@ 41 15@LB@@LB@@LB@Energy -7.18 kcal/mol@LB@Hybridization Energy -19.4847 kcal/mol@LB@Unfolding Energy - mRNA 3.10673 kcal/mol@LB@Unfolding Energy - sRNA 9.1996 kcal/mol@LB@@LB@Position - mRNA 171 -- 193@LB@Position - sRNA 16 -- 40@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 16 -- 22@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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