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
166	0.01873	0.3614	b0473	htpG	-6.61	0.137913	119 -- 133	26 -- 39	protein refolding molecular co-chaperone Hsp90 Hsp70-dependent; heat-shock protein; ATPase	_____________118_____________134\n_____________\|_______________\|\n5'-UCA...GCUCU_________UU____UCCCU...GUG-3'\n______________CGCUUGAAA__AUUC\n______________\|:\|\|\|:\|\|\|__\|\|\|\|\n______________GUGAAUUUU__UAAG\n3'-UUU...UCUUC_________U_____CAAUG...CAA-5'\n_____________\|_______________\|\n_____________40______________25\n	121 -- 127	31 -- 37	-10.0825 kcal/mol	1.82368 kcal/mol	1.64668 kcal/mol	118 134@LB@ \| \|@LB@5'-UCA...GCUCU UU UCCCU...GUG-3'@LB@ CGCUUGAAA AUUC@LB@ \|:\|\|\|:\|\|\| \|\|\|\|@LB@ GUGAAUUUU UAAG@LB@3'-UUU...UCUUC U CAAUG...CAA-5'@LB@ \| \|@LB@ 40 25@LB@@LB@@LB@Energy -6.61 kcal/mol@LB@Hybridization Energy -10.0825 kcal/mol@LB@Unfolding Energy - mRNA 1.82368 kcal/mol@LB@Unfolding Energy - sRNA 1.64668 kcal/mol@LB@@LB@Position - mRNA 119 -- 133@LB@Position - sRNA 26 -- 39@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 31 -- 37@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@
82	0.005534	0.2146	b1342	ydaN	-6.57	0.141434	180 -- 206	30 -- 54	putative Zn(II) transporter	_____________179_________________________207\n_____________\|___________________________\|\n5'-CGU...AAUAA___G____U_AU_________GU____GCGAU...AUG-3'\n______________UGC_UUGA_G__GGAGGCACU__GGAA\n______________\|\|\|_\|\|:\|_\|__:\|\|:\|\|\|\|\|__::\|\|\n______________ACG_AAUU_C__UCUUCGUGA__UUUU\n3'-UUU...UUUGA__________GU_________AU____UAAGC...CAA-5'\n_____________\|___________________________\|\n_____________55__________________________29\n	194 -- 200	36 -- 42	-19.056 kcal/mol	6.29262 kcal/mol	6.19579 kcal/mol	179 207@LB@ \| \|@LB@5'-CGU...AAUAA G U AU GU GCGAU...AUG-3'@LB@ UGC UUGA G GGAGGCACU GGAA@LB@ \|\|\| \|\|:\| \| :\|\|:\|\|\|\|\| ::\|\|@LB@ ACG AAUU C UCUUCGUGA UUUU@LB@3'-UUU...UUUGA GU AU UAAGC...CAA-5'@LB@ \| \|@LB@ 55 29@LB@@LB@@LB@Energy -6.57 kcal/mol@LB@Hybridization Energy -19.056 kcal/mol@LB@Unfolding Energy - mRNA 6.29262 kcal/mol@LB@Unfolding Energy - sRNA 6.19579 kcal/mol@LB@@LB@Position - mRNA 180 -- 206@LB@Position - sRNA 30 -- 54@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 36 -- 42@LB@
71	0.00365	0.1656	b4478	dgoD	-6.42	0.153775	171 -- 195	38 -- 57	D-galactonate dehydratase	_____________170_______________________196\n_____________\|_________________________\|\n5'-AAA...GCAGC_______A____GUAUC________GUGCA...UGA-3'\n______________AUUUGUU_AGGC_____GAGAGGCA\n______________\|:\|\|\|:\|_\|:\|\|_____:\|\|\|:\|\|\|\n______________UGAACGA_UUCG_____UUCUUCGU\n3'-UUU...UACUU_______A_________________GAAUU...CAA-5'\n_____________\|_________________________\|\n_____________58________________________37\n	189 -- 195	38 -- 44	-17.6382 kcal/mol	5.02573 kcal/mol	6.19395 kcal/mol	170 196@LB@ \| \|@LB@5'-AAA...GCAGC A GUAUC GUGCA...UGA-3'@LB@ AUUUGUU AGGC GAGAGGCA@LB@ \|:\|\|\|:\| \|:\|\| :\|\|\|:\|\|\|@LB@ UGAACGA UUCG UUCUUCGU@LB@3'-UUU...UACUU A GAAUU...CAA-5'@LB@ \| \|@LB@ 58 37@LB@@LB@@LB@Energy -6.42 kcal/mol@LB@Hybridization Energy -17.6382 kcal/mol@LB@Unfolding Energy - mRNA 5.02573 kcal/mol@LB@Unfolding Energy - sRNA 6.19395 kcal/mol@LB@@LB@Position - mRNA 171 -- 195@LB@Position - sRNA 38 -- 57@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 38 -- 44@LB@
67	0.003475	0.1645	b0416	nusB	-6.41	0.154688	140 -- 154	27 -- 40	transcription antitermination protein	_____________139_____________155\n_____________\|_______________\|\n5'-AAG...UGACC__________U____AAUGU...AGU-3'\n______________GCGCUUGAAA_GAUU\n______________\|\|:\|\|\|:\|\|\|_:\|\|\|\n______________CGUGAAUUUU_UUAA\n3'-UUU...UUCUU_______________GCAAU...CAA-5'\n_____________\|_______________\|\n_____________41______________26\n	142 -- 148	32 -- 38	-12.213 kcal/mol	4.16264 kcal/mol	1.6425 kcal/mol	139 155@LB@ \| \|@LB@5'-AAG...UGACC U AAUGU...AGU-3'@LB@ GCGCUUGAAA GAUU@LB@ \|\|:\|\|\|:\|\|\| :\|\|\|@LB@ CGUGAAUUUU UUAA@LB@3'-UUU...UUCUU GCAAU...CAA-5'@LB@ \| \|@LB@ 41 26@LB@@LB@@LB@Energy -6.41 kcal/mol@LB@Hybridization Energy -12.213 kcal/mol@LB@Unfolding Energy - mRNA 4.16264 kcal/mol@LB@Unfolding Energy - sRNA 1.6425 kcal/mol@LB@@LB@Position - mRNA 140 -- 154@LB@Position - sRNA 27 -- 40@LB@Position Seed - mRNA 142 -- 148@LB@Position Seed - sRNA 32 -- 38@LB@
51	0.002326	0.1469	b2780	pyrG	-6.37	0.158020	19 -- 28	33 -- 42	CTP synthetase	_____________18_________29\n_____________\|__________\|\n5'-UGU...AUGAC__________UUUGC...GCC-3'\n______________AAGCGCUUGA\n______________\|\|\|\|:\|\|\|:\|\n______________UUCGUGAAUU\n3'-UUU...CGUUC__________UUUUA...CAA-5'\n_____________\|__________\|\n_____________43_________32\n	22 -- 28	33 -- 39	-10.9983 kcal/mol	3.00927 kcal/mol	1.61944 kcal/mol	18 29@LB@ \| \|@LB@5'-UGU...AUGAC UUUGC...GCC-3'@LB@ AAGCGCUUGA@LB@ \|\|\|\|:\|\|\|:\|@LB@ UUCGUGAAUU@LB@3'-UUU...CGUUC UUUUA...CAA-5'@LB@ \| \|@LB@ 43 32@LB@@LB@@LB@Energy -6.37 kcal/mol@LB@Hybridization Energy -10.9983 kcal/mol@LB@Unfolding Energy - mRNA 3.00927 kcal/mol@LB@Unfolding Energy - sRNA 1.61944 kcal/mol@LB@@LB@Position - mRNA 19 -- 28@LB@Position - sRNA 33 -- 42@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 33 -- 39@LB@
60	0.00317	0.1645	b0466	ybaM	-6.37	0.157728	143 -- 158	25 -- 40	DUF2496 family protein	_____________142_______________159\n_____________\|_________________\|\n5'-GCA...GCCAU_____GG__________AAAAC...CGC-3'\n______________GCGCU__AAAAAAU_CG\n______________\|\|:\|\|__\|\|\|\|\|\|\|_\|\|\n______________CGUGA__UUUUUUA_GC\n3'-UUU...UUCUU_____A________A__AAUGU...CAA-5'\n_____________\|_________________\|\n_____________41________________24\n	150 -- 156	28 -- 34	-11.3444 kcal/mol	3.32327 kcal/mol	1.64821 kcal/mol	142 159@LB@ \| \|@LB@5'-GCA...GCCAU GG AAAAC...CGC-3'@LB@ GCGCU AAAAAAU CG@LB@ \|\|:\|\| \|\|\|\|\|\|\| \|\|@LB@ CGUGA UUUUUUA GC@LB@3'-UUU...UUCUU A A AAUGU...CAA-5'@LB@ \| \|@LB@ 41 24@LB@@LB@@LB@Energy -6.37 kcal/mol@LB@Hybridization Energy -11.3444 kcal/mol@LB@Unfolding Energy - mRNA 3.32327 kcal/mol@LB@Unfolding Energy - sRNA 1.64821 kcal/mol@LB@@LB@Position - mRNA 143 -- 158@LB@Position - sRNA 25 -- 40@LB@Position Seed - mRNA 150 -- 156@LB@Position Seed - sRNA 28 -- 34@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@
49	0.002267	0.1465	b0592	fepB	-6.35	0.159662	143 -- 160	24 -- 40	ferrienterobactin ABC transporter periplasmic binding protein	_____________142________________161\n_____________\|__________________\|\n5'-AUA...AUUGU______UGUC________CAUUA...UUA-3'\n______________GCGCUU____GAAUUUGU\n______________\|\|:\|\|\|____:\|\|\|\|:\|\|\n______________CGUGAA____UUUAAGCA\n3'-UUU...UUCUU______UUU_________AUGUG...CAA-5'\n_____________\|__________________\|\n_____________41_________________23\n	154 -- 160	24 -- 30	-12.773 kcal/mol	4.77335 kcal/mol	1.64869 kcal/mol	142 161@LB@ \| \|@LB@5'-AUA...AUUGU UGUC CAUUA...UUA-3'@LB@ GCGCUU GAAUUUGU@LB@ \|\|:\|\|\| :\|\|\|\|:\|\|@LB@ CGUGAA UUUAAGCA@LB@3'-UUU...UUCUU UUU AUGUG...CAA-5'@LB@ \| \|@LB@ 41 23@LB@@LB@@LB@Energy -6.35 kcal/mol@LB@Hybridization Energy -12.773 kcal/mol@LB@Unfolding Energy - mRNA 4.77335 kcal/mol@LB@Unfolding Energy - sRNA 1.64869 kcal/mol@LB@@LB@Position - mRNA 143 -- 160@LB@Position - sRNA 24 -- 40@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 24 -- 30@LB@
50	0.002273	0.1465	b4159	mscM	-6.32	0.162358	72 -- 90	16 -- 34	mechanosensitive channel protein miniconductance	_____________71__________________91\n_____________\|___________________\|\n5'-AAG...CUACC____CC_____________ACGCU...AGC-3'\n______________GAAA__UUUGUUACGCCAG\n______________:\|\|\|__\|\|:\|\|\|\|\|:\|\|\|\|\n______________UUUU__AAGCAAUGUGGUC\n3'-UUU...GUGAA____UU_____________CUUUA...CAA-5'\n_____________\|___________________\|\n_____________35__________________15\n	84 -- 90	16 -- 22	-19.9467 kcal/mol	4.98786 kcal/mol	8.63814 kcal/mol	71 91@LB@ \| \|@LB@5'-AAG...CUACC CC ACGCU...AGC-3'@LB@ GAAA UUUGUUACGCCAG@LB@ :\|\|\| \|\|:\|\|\|\|\|:\|\|\|\|@LB@ UUUU AAGCAAUGUGGUC@LB@3'-UUU...GUGAA UU CUUUA...CAA-5'@LB@ \| \|@LB@ 35 15@LB@@LB@@LB@Energy -6.32 kcal/mol@LB@Hybridization Energy -19.9467 kcal/mol@LB@Unfolding Energy - mRNA 4.98786 kcal/mol@LB@Unfolding Energy - sRNA 8.63814 kcal/mol@LB@@LB@Position - mRNA 72 -- 90@LB@Position - sRNA 16 -- 34@LB@Position Seed - mRNA 84 -- 90@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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