Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
158	0.01161	0.2504	b3907	rhaT	-15.90	0.016445	218 -- 234	1 -- 28	L-rhamnose:proton symporter		_____________217__________________________235\n_____________\|____________________________\|\n5'-AUG...AUUAC____________U_______________AUUUG...CAU-3'\n______________GAUGGGGAUAUU____________UGGC\n______________:\|\|\|\|\|\|\|:\|\|:____________\|\|\|\|\n______________UUACCCCUGUAG____________ACCG\n3'-UUU...GUGUU____________UUUCUUUUCGUC____-5'\n_____________\|___________________________\|\n_____________29__________________________1\n	223 -- 229	17 -- 23	-20.3321 kcal/mol	1.91011 kcal/mol	2.519 kcal/mol	217 235@LB@ \| \|@LB@5'-AUG...AUUAC U AUUUG...CAU-3'@LB@ GAUGGGGAUAUU UGGC@LB@ :\|\|\|\|\|\|\|:\|\|: \|\|\|\|@LB@ UUACCCCUGUAG ACCG@LB@3'-UUU...GUGUU UUUCUUUUCGUC -5'@LB@ \| \|@LB@ 29 1@LB@@LB@@LB@Energy -15.90 kcal/mol@LB@Hybridization Energy -20.3321 kcal/mol@LB@Unfolding Energy - mRNA 1.91011 kcal/mol@LB@Unfolding Energy - sRNA 2.519 kcal/mol@LB@@LB@Position - mRNA 218 -- 234@LB@Position - sRNA 1 -- 28@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 17 -- 23@LB@
37	0.001785	0.1648	b3933	ftsN	-15.64	0.019200	24 -- 52	1 -- 29	essential cell division protein		_____________23______________________________53\n_____________\|_______________________________\|\n5'-AGC...UGAUC_____CA______A__CGUU___________UCUCG...CUC-3'\n______________AAAUG__GGGGCA_CA______GGCAGUGGC\n______________\|\|\|\|\|__\|\|\|:\|\|_\|\|______:\|\|\|\|\|\|\|\|\n______________UUUAC__CCCUGU_GU______UCGUCACCG\n3'-UUU...GGUGU_____________A__UUCUUU_________-5'\n_____________\|______________________________\|\n_____________30_____________________________1\n	46 -- 52	1 -- 7	-29.0551 kcal/mol	10.8938 kcal/mol	2.51907 kcal/mol	23 53@LB@ \| \|@LB@5'-AGC...UGAUC CA A CGUU UCUCG...CUC-3'@LB@ AAAUG GGGGCA CA GGCAGUGGC@LB@ \|\|\|\|\| \|\|\|:\|\| \|\| :\|\|\|\|\|\|\|\|@LB@ UUUAC CCCUGU GU UCGUCACCG@LB@3'-UUU...GGUGU A UUCUUU -5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -15.64 kcal/mol@LB@Hybridization Energy -29.0551 kcal/mol@LB@Unfolding Energy - mRNA 10.8938 kcal/mol@LB@Unfolding Energy - sRNA 2.51907 kcal/mol@LB@@LB@Position - mRNA 24 -- 52@LB@Position - sRNA 1 -- 29@LB@Position Seed - mRNA 46 -- 52@LB@Position Seed - sRNA 1 -- 7@LB@
91	0.005641	0.2147	b3956	ppc	-14.82	0.030673	242 -- 282	2 -- 37	phosphoenolpyruvate carboxylase		_____________241_________________________________________283\n_____________\|___________________________________________\|\n5'-CUU...AGUAU____G________CU____GAAAC_________U_____U___GAGAA...AAC-3'\n______________GCUC_GCAAAGUG__GGGA_____CAUCAAGGA___GCG_UGG\n______________\|\|\|\|_:\|\|\|\|:\|\|__\|\|\|\|_____\|\|\|\|\|\|:\|\|___\|\|:_\|\|\|\n______________CGAG_UGUUUUAC__CCCU_____GUAGUUUCU___CGU_ACC\n3'-UUU...CUACC____G____________________________UUU___C___G-5'\n_____________\|___________________________________________\|\n_____________38__________________________________________1\n	268 -- 274	12 -- 18	-37.6415 kcal/mol	13.2441 kcal/mol	9.57751 kcal/mol	241 283@LB@ \| \|@LB@5'-CUU...AGUAU G CU GAAAC U U GAGAA...AAC-3'@LB@ GCUC GCAAAGUG GGGA CAUCAAGGA GCG UGG@LB@ \|\|\|\| :\|\|\|\|:\|\| \|\|\|\| \|\|\|\|\|\|:\|\| \|\|: \|\|\|@LB@ CGAG UGUUUUAC CCCU GUAGUUUCU CGU ACC@LB@3'-UUU...CUACC G UUU C G-5'@LB@ \| \|@LB@ 38 1@LB@@LB@@LB@Energy -14.82 kcal/mol@LB@Hybridization Energy -37.6415 kcal/mol@LB@Unfolding Energy - mRNA 13.2441 kcal/mol@LB@Unfolding Energy - sRNA 9.57751 kcal/mol@LB@@LB@Position - mRNA 242 -- 282@LB@Position - sRNA 2 -- 37@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 12 -- 18@LB@
176	0.01279	0.2504	b3980	tufB	-13.59	0.058494	200 -- 216	7 -- 22	translation elongation factor EF-Tu 2	b3339	_____________199_______________217\n_____________\|_________________\|\n5'-UCC...CAAUC______U__________UUGAA...CUA-3'\n______________GAUGUC_AAAGAAAAGU\n______________\|\|::\|\|_\|\|\|\|\|\|\|\|\|:\n______________CUGUAG_UUUCUUUUCG\n3'-UUU...UACCC_________________UCACCG-5'\n_____________\|_________________\|\n_____________23________________6\n	210 -- 216	7 -- 13	-16.0105 kcal/mol	1.82662 kcal/mol	0.590875 kcal/mol	199 217@LB@ \| \|@LB@5'-UCC...CAAUC U UUGAA...CUA-3'@LB@ GAUGUC AAAGAAAAGU@LB@ \|\|::\|\| \|\|\|\|\|\|\|\|\|:@LB@ CUGUAG UUUCUUUUCG@LB@3'-UUU...UACCC UCACCG-5'@LB@ \| \|@LB@ 23 6@LB@@LB@@LB@Energy -13.59 kcal/mol@LB@Hybridization Energy -16.0105 kcal/mol@LB@Unfolding Energy - mRNA 1.82662 kcal/mol@LB@Unfolding Energy - sRNA 0.590875 kcal/mol@LB@@LB@Position - mRNA 200 -- 216@LB@Position - sRNA 7 -- 22@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 7 -- 13@LB@
142	0.01047	0.2504	b3998	nfi	-11.68	0.142276	34 -- 51	5 -- 21	endonuclease V; deoxyinosine 3' endonuclease		_____________33_________________52\n_____________\|__________________\|\n5'-UGG...UGCCC_________A________CGACU...GAG-3'\n______________GCAUUGAAG_AGAAGUAG\n______________:\|\|\|::\|\|\|_\|:\|\|\|:\|\|\n______________UGUAGUUUC_UUUUCGUC\n3'-UUU...ACCCC__________________ACCG-5'\n_____________\|__________________\|\n_____________22_________________4\n	45 -- 51	5 -- 11	-17.0993 kcal/mol	3.91468 kcal/mol	1.5073 kcal/mol	33 52@LB@ \| \|@LB@5'-UGG...UGCCC A CGACU...GAG-3'@LB@ GCAUUGAAG AGAAGUAG@LB@ :\|\|\|::\|\|\| \|:\|\|\|:\|\|@LB@ UGUAGUUUC UUUUCGUC@LB@3'-UUU...ACCCC ACCG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -11.68 kcal/mol@LB@Hybridization Energy -17.0993 kcal/mol@LB@Unfolding Energy - mRNA 3.91468 kcal/mol@LB@Unfolding Energy - sRNA 1.5073 kcal/mol@LB@@LB@Position - mRNA 34 -- 51@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 5 -- 11@LB@
9	0.0002541	0.09908	b4000	hupA	-15.77	0.017828	82 -- 110	1 -- 35	HU DNA-binding transcriptional regulator alpha subunit		_____________81__________________________________111\n_____________\|___________________________________\|\n5'-UUU...UCUGG______UUUG_________________AA______UAUCG...CUG-3'\n______________UCUACA____GGGGGCG______AAAA__AGUGGC\n______________\|\|:\|\|\|____\|\|\|\|:\|:______\|\|\|\|__\|\|\|\|\|\|\n______________AGGUGU____CCCCUGU______UUUU__UCACCG\n3'-UUU...ACCCG______UUUA_______AGUUUC____CG______-5'\n_____________\|__________________________________\|\n_____________36_________________________________1\n	92 -- 98	19 -- 25	-28.6527 kcal/mol	7.84855 kcal/mol	5.03645 kcal/mol	81 111@LB@ \| \|@LB@5'-UUU...UCUGG UUUG AA UAUCG...CUG-3'@LB@ UCUACA GGGGGCG AAAA AGUGGC@LB@ \|\|:\|\|\| \|\|\|\|:\|: \|\|\|\| \|\|\|\|\|\|@LB@ AGGUGU CCCCUGU UUUU UCACCG@LB@3'-UUU...ACCCG UUUA AGUUUC CG -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -15.77 kcal/mol@LB@Hybridization Energy -28.6527 kcal/mol@LB@Unfolding Energy - mRNA 7.84855 kcal/mol@LB@Unfolding Energy - sRNA 5.03645 kcal/mol@LB@@LB@Position - mRNA 82 -- 110@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 92 -- 98@LB@Position Seed - sRNA 19 -- 25@LB@
105	0.007004	0.2333	b4034	malE	-12.62	0.093531	92 -- 123	2 -- 32	maltose transporter subunit		_____________91_________________________________124\n_____________\|__________________________________\|\n5'-AGG...ACAAA____C_________________C___G__GA___AAAGA...UGG-3'\n______________GCGA_GGUGGGG_CGU_AGGGG_AAG_AG__UGG\n______________:\|:\|_::\|\|\|\|\|_\|:\|_\|::\|:_\|\|\|_\|\|__\|\|\|\n______________UGUU_UUACCCC_GUA_UUUCU_UUC_UC__ACC\n3'-UUU...CGAGG____________U___G_____U___G_______G-5'\n_____________\|__________________________________\|\n_____________33_________________________________1\n	97 -- 103	22 -- 28	-24.1065 kcal/mol	8.94734 kcal/mol	2.53929 kcal/mol	91 124@LB@ \| \|@LB@5'-AGG...ACAAA C C G GA AAAGA...UGG-3'@LB@ GCGA GGUGGGG CGU AGGGG AAG AG UGG@LB@ :\|:\| ::\|\|\|\|\| \|:\| \|::\|: \|\|\| \|\| \|\|\|@LB@ UGUU UUACCCC GUA UUUCU UUC UC ACC@LB@3'-UUU...CGAGG U G U G G-5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -12.62 kcal/mol@LB@Hybridization Energy -24.1065 kcal/mol@LB@Unfolding Energy - mRNA 8.94734 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 92 -- 123@LB@Position - sRNA 2 -- 32@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 22 -- 28@LB@
27	0.001238	0.1512	b4045	yjbJ	-9.99	0.275707	259 -- 267	19 -- 28	stress-induced protein UPF0337 family		_____________258________268\n_____________\|__________\|\n5'-CGU...AGAGC__________AACUG...AAG-3'\n______________AAUGGGG_CA\n______________\|\|\|\|\|\|\|_\|\|\n______________UUACCCC_GU\n3'-UUU...GUGUU_______U__AGUUU...CCG-5'\n_____________\|__________\|\n_____________29_________18\n	259 -- 265	22 -- 28	-11.8839 kcal/mol	1.24365 kcal/mol	0.649553 kcal/mol	258 268@LB@ \| \|@LB@5'-CGU...AGAGC AACUG...AAG-3'@LB@ AAUGGGG CA@LB@ \|\|\|\|\|\|\| \|\|@LB@ UUACCCC GU@LB@3'-UUU...GUGUU U AGUUU...CCG-5'@LB@ \| \|@LB@ 29 18@LB@@LB@@LB@Energy -9.99 kcal/mol@LB@Hybridization Energy -11.8839 kcal/mol@LB@Unfolding Energy - mRNA 1.24365 kcal/mol@LB@Unfolding Energy - sRNA 0.649553 kcal/mol@LB@@LB@Position - mRNA 259 -- 267@LB@Position - sRNA 19 -- 28@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 22 -- 28@LB@
136	0.00981	0.2504	b4063	soxR	-14.24	0.041834	39 -- 60	1 -- 21	redox-sensitive transcriptional activator of soxS; autorepressor		_____________38_____________________61\n_____________\|______________________\|\n5'-GCA...CGACU_______U_UU______C____CAAUA...GUA-3'\n______________ACAUCAA_G__AAGCGG_UGGU\n______________\|\|\|\|\|\|\|_\|__\|\|\|\|:\|_\|\|\|:\n______________UGUAGUU_C__UUCGUC_ACCG\n3'-UUU...ACCCC_______U_UU___________-5'\n_____________\|_____________________\|\n_____________22____________________1\n	39 -- 45	15 -- 21	-21.0533 kcal/mol	5.29766 kcal/mol	1.51103 kcal/mol	38 61@LB@ \| \|@LB@5'-GCA...CGACU U UU C CAAUA...GUA-3'@LB@ ACAUCAA G AAGCGG UGGU@LB@ \|\|\|\|\|\|\| \| \|\|\|\|:\| \|\|\|:@LB@ UGUAGUU C UUCGUC ACCG@LB@3'-UUU...ACCCC U UU -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -14.24 kcal/mol@LB@Hybridization Energy -21.0533 kcal/mol@LB@Unfolding Energy - mRNA 5.29766 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 39 -- 60@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 15 -- 21@LB@
59	0.003042	0.1789	b4132	cadB	-12.03	0.121895	256 -- 272	4 -- 32	putative lysine/cadaverine transporter		_____________255___________________________273\n_____________\|_____________________________\|\n5'-UCA...CGGUA___U_________________________AUUGC...CAA-3'\n______________AUA_GAUGGGGA____________GCGGU\n______________\|:\|_:\|\|\|\|\|\|\|____________\|\|:\|\|\n______________UGU_UUACCCCU____________CGUCA\n3'-UUU...CGAGG___U________GUAGUUUCUUUU_____CCG-5'\n_____________\|_____________________________\|\n_____________33____________________________3\n	261 -- 267	21 -- 27	-16.7324 kcal/mol	2.16267 kcal/mol	2.53583 kcal/mol	255 273@LB@ \| \|@LB@5'-UCA...CGGUA U AUUGC...CAA-3'@LB@ AUA GAUGGGGA GCGGU@LB@ \|:\| :\|\|\|\|\|\|\| \|\|:\|\|@LB@ UGU UUACCCCU CGUCA@LB@3'-UUU...CGAGG U GUAGUUUCUUUU CCG-5'@LB@ \| \|@LB@ 33 3@LB@@LB@@LB@Energy -12.03 kcal/mol@LB@Hybridization Energy -16.7324 kcal/mol@LB@Unfolding Energy - mRNA 2.16267 kcal/mol@LB@Unfolding Energy - sRNA 2.53583 kcal/mol@LB@@LB@Position - mRNA 256 -- 272@LB@Position - sRNA 4 -- 32@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 21 -- 27@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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