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
191	0.02253	0.38	b3186	rplU	-5.10	0.305418	95 -- 102	34 -- 41	50S ribosomal subunit protein L21	_____________94_______103\n_____________\|________\|\n5'-UUA...ACUGU________UCAAA...UUG-3'\n______________AGCACUUG\n______________\|\|\|\|\|\|\|:\n______________UCGUGAAU\n3'-UUU...GUUCU________UUUUU...CAA-5'\n_____________\|________\|\n_____________42_______33\n	96 -- 102	34 -- 40	-9.60207 kcal/mol	2.88333 kcal/mol	1.6155 kcal/mol	94 103@LB@ \| \|@LB@5'-UUA...ACUGU UCAAA...UUG-3'@LB@ AGCACUUG@LB@ \|\|\|\|\|\|\|:@LB@ UCGUGAAU@LB@3'-UUU...GUUCU UUUUU...CAA-5'@LB@ \| \|@LB@ 42 33@LB@@LB@@LB@Energy -5.10 kcal/mol@LB@Hybridization Energy -9.60207 kcal/mol@LB@Unfolding Energy - mRNA 2.88333 kcal/mol@LB@Unfolding Energy - sRNA 1.6155 kcal/mol@LB@@LB@Position - mRNA 95 -- 102@LB@Position - sRNA 34 -- 41@LB@Position Seed - mRNA 96 -- 102@LB@Position Seed - sRNA 34 -- 40@LB@
192	0.02295	0.3851	b1282	yciH	-4.88	0.338940	8 -- 32	15 -- 33	initiation factor function partial mimic SUI1 family	_____________7_________________________33\n_____________\|_________________________\|\n____5'-UUCGGUC________AAACUG___________CAUUC...UGC-3'\n______________AGGAGUUC______GUUACGCCGGG\n______________\|::\|:\|\|\|______\|\|\|\|\|:\|\|:\|\|\n______________UUUUUAAG______CAAUGUGGUCC\n3'-UUU...UGAAU_________________________UUUAG...CAA-5'\n_____________\|_________________________\|\n_____________34________________________14\n	9 -- 15	26 -- 32	-19.9664 kcal/mol	6.44674 kcal/mol	8.63649 kcal/mol	7 33@LB@ \| \|@LB@ 5'-UUCGGUC AAACUG CAUUC...UGC-3'@LB@ AGGAGUUC GUUACGCCGGG@LB@ \|::\|:\|\|\| \|\|\|\|\|:\|\|:\|\|@LB@ UUUUUAAG CAAUGUGGUCC@LB@3'-UUU...UGAAU UUUAG...CAA-5'@LB@ \| \|@LB@ 34 14@LB@@LB@@LB@Energy -4.88 kcal/mol@LB@Hybridization Energy -19.9664 kcal/mol@LB@Unfolding Energy - mRNA 6.44674 kcal/mol@LB@Unfolding Energy - sRNA 8.63649 kcal/mol@LB@@LB@Position - mRNA 8 -- 32@LB@Position - sRNA 15 -- 33@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 26 -- 32@LB@
193	0.0233	0.3864	b1563	relE	-9.36	0.025073	16 -- 27	29 -- 40	Qin prophage; toxin of the RelE-RelB toxin-antitoxin system	_____________15___________28\n_____________\|____________\|\n5'-GCG...ACGCC____________AUGGG...UAC-3'\n______________GCGCUUGAAAAA\n______________\|\|:\|\|\|:\|\|\|\|\|\n______________CGUGAAUUUUUU\n3'-UUU...UUCUU____________AAGCA...CAA-5'\n_____________\|____________\|\n_____________41___________28\n	21 -- 27	29 -- 35	-12.3855 kcal/mol	1.40487 kcal/mol	1.62106 kcal/mol	15 28@LB@ \| \|@LB@5'-GCG...ACGCC AUGGG...UAC-3'@LB@ GCGCUUGAAAAA@LB@ \|\|:\|\|\|:\|\|\|\|\|@LB@ CGUGAAUUUUUU@LB@3'-UUU...UUCUU AAGCA...CAA-5'@LB@ \| \|@LB@ 41 28@LB@@LB@@LB@Energy -9.36 kcal/mol@LB@Hybridization Energy -12.3855 kcal/mol@LB@Unfolding Energy - mRNA 1.40487 kcal/mol@LB@Unfolding Energy - sRNA 1.62106 kcal/mol@LB@@LB@Position - mRNA 16 -- 27@LB@Position - sRNA 29 -- 40@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 29 -- 35@LB@
194	0.02335	0.3864	b4182	yjfJ	-9.08	0.030148	209 -- 238	10 -- 37	PspA/IM30 family protein	_____________208____________________________239\n_____________\|______________________________\|\n5'-GAA...GGAAU____________AU______UG________GUUUA...AGC-3'\n______________UUUAAAAAGUUU__UUACGC__GGGAAAUC\n______________:\|\|\|\|\|\|\|:\|\|:__\|\|\|\|:\|__:\|\|\|\|\|\|\|\n______________GAAUUUUUUAAG__AAUGUG__UCCUUUAG\n3'-UUU...UUCGU____________C_______G_________ACUAC...CAA-5'\n_____________\|______________________________\|\n_____________38_____________________________9\n	232 -- 238	10 -- 16	-23.4786 kcal/mol	5.49388 kcal/mol	8.90309 kcal/mol	208 239@LB@ \| \|@LB@5'-GAA...GGAAU AU UG GUUUA...AGC-3'@LB@ UUUAAAAAGUUU UUACGC GGGAAAUC@LB@ :\|\|\|\|\|\|\|:\|\|: \|\|\|\|:\| :\|\|\|\|\|\|\|@LB@ GAAUUUUUUAAG AAUGUG UCCUUUAG@LB@3'-UUU...UUCGU C G ACUAC...CAA-5'@LB@ \| \|@LB@ 38 9@LB@@LB@@LB@Energy -9.08 kcal/mol@LB@Hybridization Energy -23.4786 kcal/mol@LB@Unfolding Energy - mRNA 5.49388 kcal/mol@LB@Unfolding Energy - sRNA 8.90309 kcal/mol@LB@@LB@Position - mRNA 209 -- 238@LB@Position - sRNA 10 -- 37@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 10 -- 16@LB@
195	0.02349	0.3864	b3982	nusG	-7.66	0.074558	21 -- 55	24 -- 55	transcription termination factor	_____________20__________________________________56\n_____________\|___________________________________\|\n5'-GAC...UACCG______UU__CCGU_______GUACC_____C___AAGGU...ACA-3'\n______________UUGCUU__GC____GAAGCGC_____GAAGU_CGU\n______________\|\|\|\|\|\|__\|\|____\|\|\|\|\|:\|_____:\|\|:\|_\|\|\|\n______________AACGAA__CG____CUUCGUG_____UUUUA_GCA\n3'-UUU...CUUUG______UU__UU_________AAUU______A___AUGUG...CAA-5'\n_____________\|___________________________________\|\n_____________56__________________________________23\n	35 -- 41	37 -- 43	-23.8738 kcal/mol	9.94572 kcal/mol	6.27216 kcal/mol	20 56@LB@ \| \|@LB@5'-GAC...UACCG UU CCGU GUACC C AAGGU...ACA-3'@LB@ UUGCUU GC GAAGCGC GAAGU CGU@LB@ \|\|\|\|\|\| \|\| \|\|\|\|\|:\| :\|\|:\| \|\|\|@LB@ AACGAA CG CUUCGUG UUUUA GCA@LB@3'-UUU...CUUUG UU UU AAUU A AUGUG...CAA-5'@LB@ \| \|@LB@ 56 23@LB@@LB@@LB@Energy -7.66 kcal/mol@LB@Hybridization Energy -23.8738 kcal/mol@LB@Unfolding Energy - mRNA 9.94572 kcal/mol@LB@Unfolding Energy - sRNA 6.27216 kcal/mol@LB@@LB@Position - mRNA 21 -- 55@LB@Position - sRNA 24 -- 55@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 37 -- 43@LB@
196	0.02353	0.3864	b1948	fliP	-9.61	0.021211	171 -- 185	45 -- 59	flagellar biosynthesis protein	_____________170_____________186\n_____________\|_______________\|\n5'-AUU...AUGAA_______________UAGCG...GCG-3'\n______________AAAUUUGCUUAAGCG\n______________\|\|\|:\|\|\|\|\|\|\|\|\|\|:\n______________UUUGAACGAAUUCGU\n3'-UUU...CCUAC_______________UCUUC...CAA-5'\n_____________\|_______________\|\n_____________60______________44\n	178 -- 184	46 -- 52	-18.3894 kcal/mol	2.75936 kcal/mol	6.02152 kcal/mol	170 186@LB@ \| \|@LB@5'-AUU...AUGAA UAGCG...GCG-3'@LB@ AAAUUUGCUUAAGCG@LB@ \|\|\|:\|\|\|\|\|\|\|\|\|\|:@LB@ UUUGAACGAAUUCGU@LB@3'-UUU...CCUAC UCUUC...CAA-5'@LB@ \| \|@LB@ 60 44@LB@@LB@@LB@Energy -9.61 kcal/mol@LB@Hybridization Energy -18.3894 kcal/mol@LB@Unfolding Energy - mRNA 2.75936 kcal/mol@LB@Unfolding Energy - sRNA 6.02152 kcal/mol@LB@@LB@Position - mRNA 171 -- 185@LB@Position - sRNA 45 -- 59@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 46 -- 52@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@
198	0.02375	0.3864	b3946	fsaB	-8.18	0.053967	105 -- 117	26 -- 40	fructose-6-phosphate aldolase 2	_____________104_____________118\n_____________\|_______________\|\n5'-UGG...AUCAU_______________CGUAA...CUG-3'\n______________GCAC__GAAGAAUUC\n______________\|\|\|\|__:\|\|:\|\|\|\|\|\n______________CGUG__UUUUUUAAG\n3'-UUU...UUCUU____AA_________CAAUG...CAA-5'\n_____________\|_______________\|\n_____________41______________25\n	111 -- 117	26 -- 32	-11.851 kcal/mol	2.02524 kcal/mol	1.64811 kcal/mol	104 118@LB@ \| \|@LB@5'-UGG...AUCAU CGUAA...CUG-3'@LB@ GCAC GAAGAAUUC@LB@ \|\|\|\| :\|\|:\|\|\|\|\|@LB@ CGUG UUUUUUAAG@LB@3'-UUU...UUCUU AA CAAUG...CAA-5'@LB@ \| \|@LB@ 41 25@LB@@LB@@LB@Energy -8.18 kcal/mol@LB@Hybridization Energy -11.851 kcal/mol@LB@Unfolding Energy - mRNA 2.02524 kcal/mol@LB@Unfolding Energy - sRNA 1.64811 kcal/mol@LB@@LB@Position - mRNA 105 -- 117@LB@Position - sRNA 26 -- 40@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 26 -- 32@LB@
199	0.02405	0.3893	b2412	zipA	-4.86	0.342002	121 -- 136	25 -- 40	FtsZ stabilizer	_____________120______________137\n_____________\|________________\|\n5'-CAG...CACUU__________UAA___GCAAA...CUU-3'\n______________GCACUUGAGG___UCG\n______________\|\|\|\|\|\|:\|::___\|\|\|\n______________CGUGAAUUUU___AGC\n3'-UUU...UUCUU__________UUA___AAUGU...CAA-5'\n_____________\|________________\|\n_____________41_______________24\n	124 -- 130	31 -- 37	-13.2366 kcal/mol	6.7246 kcal/mol	1.64821 kcal/mol	120 137@LB@ \| \|@LB@5'-CAG...CACUU UAA GCAAA...CUU-3'@LB@ GCACUUGAGG UCG@LB@ \|\|\|\|\|\|:\|:: \|\|\|@LB@ CGUGAAUUUU AGC@LB@3'-UUU...UUCUU UUA AAUGU...CAA-5'@LB@ \| \|@LB@ 41 24@LB@@LB@@LB@Energy -4.86 kcal/mol@LB@Hybridization Energy -13.2366 kcal/mol@LB@Unfolding Energy - mRNA 6.7246 kcal/mol@LB@Unfolding Energy - sRNA 1.64821 kcal/mol@LB@@LB@Position - mRNA 121 -- 136@LB@Position - sRNA 25 -- 40@LB@Position Seed - mRNA 124 -- 130@LB@Position Seed - sRNA 31 -- 37@LB@
200	0.02417	0.3893	b1747	astA	-6.36	0.159223	49 -- 56	39 -- 46	arginine succinyltransferase	_____________48_______57\n_____________\|________\|\n5'-GGC...UCUCU________GGCGA...AAG-3'\n______________CAGGAAGC\n______________\|\|:\|\|\|\|\|\n______________GUUCUUCG\n3'-UUU...AAUUC________UGAAU...CAA-5'\n_____________\|________\|\n_____________47_______38\n	50 -- 56	39 -- 45	-10.5455 kcal/mol	1.56403 kcal/mol	2.62555 kcal/mol	48 57@LB@ \| \|@LB@5'-GGC...UCUCU GGCGA...AAG-3'@LB@ CAGGAAGC@LB@ \|\|:\|\|\|\|\|@LB@ GUUCUUCG@LB@3'-UUU...AAUUC UGAAU...CAA-5'@LB@ \| \|@LB@ 47 38@LB@@LB@@LB@Energy -6.36 kcal/mol@LB@Hybridization Energy -10.5455 kcal/mol@LB@Unfolding Energy - mRNA 1.56403 kcal/mol@LB@Unfolding Energy - sRNA 2.62555 kcal/mol@LB@@LB@Position - mRNA 49 -- 56@LB@Position - sRNA 39 -- 46@LB@Position Seed - mRNA 50 -- 56@LB@Position Seed - sRNA 39 -- 45@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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