Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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
12	4.171e-05	0.01168	b0814	ompX	-14.35	0.017131	192 -- 226	1 -- 48	outer membrane protein X	_____________191______________________________________________227\n_____________\|________________________________________________\|\n5'-CUG...CAUUU_________A___AAAAAAAUU__________________C_______ACUGG...CAC-3'\n______________GAGGUGGUU__UG_________GCA____________UGU_UUUCAGC\n______________\|\|\|\|\|\|\|\|\|__\|\|_________\|\|\|____________\|\|\|_\|\|\|\|\|\|\|\n______________CUCCACCAA__AC_________CGU____________ACA_AAAGUCG\n3'-UUU...GAUUC_________GG__CAUGUCGAU___AAAAUACCCAAU___A_______-5'\n_____________\|_______________________________________________\|\n_____________49______________________________________________1\n	220 -- 226	1 -- 7	-27.166 kcal/mol	8.20777 kcal/mol	4.60955 kcal/mol	191 227@LB@ \| \|@LB@5'-CUG...CAUUU A AAAAAAAUU C ACUGG...CAC-3'@LB@ GAGGUGGUU UG GCA UGU UUUCAGC@LB@ \|\|\|\|\|\|\|\|\| \|\| \|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ CUCCACCAA AC CGU ACA AAAGUCG@LB@3'-UUU...GAUUC GG CAUGUCGAU AAAAUACCCAAU A -5'@LB@ \| \|@LB@ 49 1@LB@@LB@@LB@Energy -14.35 kcal/mol@LB@Hybridization Energy -27.166 kcal/mol@LB@Unfolding Energy - mRNA 8.20777 kcal/mol@LB@Unfolding Energy - sRNA 4.60955 kcal/mol@LB@@LB@Position - mRNA 192 -- 226@LB@Position - sRNA 1 -- 48@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 1 -- 7@LB@
123	0.005173	0.1413	b0839	dacC	-12.36	0.054489	29 -- 38	24 -- 33	D-alanyl-D-alanine carboxypeptidase; penicillin-binding protein 6a	_____________28_________39\n_____________\|__________\|\n5'-AUG...AAGCA__________AAAAA...AAG-3'\n______________ACAGCUGGCA\n______________\|\|\|\|\|\|:\|\|\|\n______________UGUCGAUCGU\n3'-UUU...GACCA__________AAAAU...UCG-5'\n_____________\|__________\|\n_____________34_________23\n	32 -- 38	24 -- 30	-17.0494 kcal/mol	3.2632 kcal/mol	1.42716 kcal/mol	28 39@LB@ \| \|@LB@5'-AUG...AAGCA AAAAA...AAG-3'@LB@ ACAGCUGGCA@LB@ \|\|\|\|\|\|:\|\|\|@LB@ UGUCGAUCGU@LB@3'-UUU...GACCA AAAAU...UCG-5'@LB@ \| \|@LB@ 34 23@LB@@LB@@LB@Energy -12.36 kcal/mol@LB@Hybridization Energy -17.0494 kcal/mol@LB@Unfolding Energy - mRNA 3.2632 kcal/mol@LB@Unfolding Energy - sRNA 1.42716 kcal/mol@LB@@LB@Position - mRNA 29 -- 38@LB@Position - sRNA 24 -- 33@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 24 -- 30@LB@
59	0.00143	0.08147	b0848	ybjM	-6.77	0.507403	86 -- 118	1 -- 33	inner membrane protein	_____________85_________________________________119\n_____________\|__________________________________\|\n5'-GAA...UAUCA___________GAAU__C____GCCUAUA_____AUGGA...GGG-3'\n______________ACGGCUA_UAU____UG_GUUG_______UUAGC\n______________\|\|:\|\|\|\|_:\|\|____\|\|_\|\|\|:_______\|:\|\|\|\n______________UGUCGAU_GUA____AC_CAAU_______AGUCG\n3'-UUU...GACCA_______C___AAAU__C____ACAAAA______-5'\n_____________\|_________________________________\|\n_____________34________________________________1\n	86 -- 92	27 -- 33	-17.6492 kcal/mol	9.38597 kcal/mol	1.49313 kcal/mol	85 119@LB@ \| \|@LB@5'-GAA...UAUCA GAAU C GCCUAUA AUGGA...GGG-3'@LB@ ACGGCUA UAU UG GUUG UUAGC@LB@ \|\|:\|\|\|\| :\|\| \|\| \|\|\|: \|:\|\|\|@LB@ UGUCGAU GUA AC CAAU AGUCG@LB@3'-UUU...GACCA C AAAU C ACAAAA -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -6.77 kcal/mol@LB@Hybridization Energy -17.6492 kcal/mol@LB@Unfolding Energy - mRNA 9.38597 kcal/mol@LB@Unfolding Energy - sRNA 1.49313 kcal/mol@LB@@LB@Position - mRNA 86 -- 118@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 86 -- 92@LB@Position Seed - sRNA 27 -- 33@LB@
45	0.001037	0.07744	b0857	potI	-11.49	0.084883	37 -- 88	3 -- 46	putrescine ABC transporter permease	_____________36______________________________________________________89\n_____________\|_______________________________________________________\|\n5'-CCG...UGCUC_________C________AUCAUGAUCGGGC____GC_____CAAGA________AUAAC...AUU-3'\n______________GGUGG__CC_GG_ACAGC_____________GCGU__UAUGG_____GUUUUUCA\n______________\|\|\|\|\|__\|\|_\|\|_\|\|\|\|\|_____________\|\|:\|__\|\|\|\|\|_____\|\|\|\|\|\|\|\|\n______________CCACC__GG_CC_UGUCG_____________CGUA__AUACC_____CAAAAAGU\n3'-UUU...UUCCU_____AA__A__A_____AU_______________AA_____CAAUA________CG-5'\n_____________\|_______________________________________________________\|\n_____________47______________________________________________________2\n	82 -- 88	3 -- 9	-33.7321 kcal/mol	17.6344 kcal/mol	4.60931 kcal/mol	36 89@LB@ \| \|@LB@5'-CCG...UGCUC C AUCAUGAUCGGGC GC CAAGA AUAAC...AUU-3'@LB@ GGUGG CC GG ACAGC GCGU UAUGG GUUUUUCA@LB@ \|\|\|\|\| \|\| \|\| \|\|\|\|\| \|\|:\| \|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ CCACC GG CC UGUCG CGUA AUACC CAAAAAGU@LB@3'-UUU...UUCCU AA A A AU AA CAAUA CG-5'@LB@ \| \|@LB@ 47 2@LB@@LB@@LB@Energy -11.49 kcal/mol@LB@Hybridization Energy -33.7321 kcal/mol@LB@Unfolding Energy - mRNA 17.6344 kcal/mol@LB@Unfolding Energy - sRNA 4.60931 kcal/mol@LB@@LB@Position - mRNA 37 -- 88@LB@Position - sRNA 3 -- 46@LB@Position Seed - mRNA 82 -- 88@LB@Position Seed - sRNA 3 -- 9@LB@
53	0.001234	0.07744	b0884	infA	-13.12	0.035785	57 -- 86	2 -- 40	translation initiation factor IF-1	_____________56_______________________________________87\n_____________\|________________________________________\|\n5'-UUU...UGCGC____________U____CG_____________________AGUAA...CUG-3'\n______________UUUUGGUGCGGC_UAGC___________UGUG_UUUUCGG\n______________\|::\|\|\|\|:\|:\|\|_\|\|\|\|___________\|:\|\|_\|\|\|\|\|:\|\n______________AGGACCAUGUCG_AUCG___________AUAC_AAAAGUC\n3'-UUU...CACCA_________________UAAAAUACCCA____A_______G-5'\n_____________\|________________________________________\|\n_____________41_______________________________________1\n	80 -- 86	2 -- 8	-28.8253 kcal/mol	11.0921 kcal/mol	4.60818 kcal/mol	56 87@LB@ \| \|@LB@5'-UUU...UGCGC U CG AGUAA...CUG-3'@LB@ UUUUGGUGCGGC UAGC UGUG UUUUCGG@LB@ \|::\|\|\|\|:\|:\|\| \|\|\|\| \|:\|\| \|\|\|\|\|:\|@LB@ AGGACCAUGUCG AUCG AUAC AAAAGUC@LB@3'-UUU...CACCA UAAAAUACCCA A G-5'@LB@ \| \|@LB@ 41 1@LB@@LB@@LB@Energy -13.12 kcal/mol@LB@Hybridization Energy -28.8253 kcal/mol@LB@Unfolding Energy - mRNA 11.0921 kcal/mol@LB@Unfolding Energy - sRNA 4.60818 kcal/mol@LB@@LB@Position - mRNA 57 -- 86@LB@Position - sRNA 2 -- 40@LB@Position Seed - mRNA 80 -- 86@LB@Position Seed - sRNA 2 -- 8@LB@
7	1.492e-05	0.007162	b0903	pflB	-20.16	0.000088	81 -- 115	14 -- 49	formate C-acetyltransferase 1 anaerobic; pyruvate formate-lyase 1	_____________80____________________________________116\n_____________\|_____________________________________\|\n5'-CAC...UUAUC__U________GU____UG_____A___AC_______CAUUU...ACU-3'\n______________GG_GGUGGUUU__UGGU__GGUUG_CAU____UGGGU\n______________\|\|_\|\|\|\|\|\|\|:__\|\|\|\|__:\|:\|:_\|\|\|____\|\|\|\|\|\n______________CC_CCACCAAG__ACCA__UCGAU_GUA____ACCCA\n3'-UUU...CGAUU__U________G_____UG_____C___AAAU_____AUACA...UCG-5'\n_____________\|_____________________________________\|\n_____________50____________________________________13\n	85 -- 91	39 -- 45	-33.3931 kcal/mol	8.66349 kcal/mol	4.57395 kcal/mol	80 116@LB@ \| \|@LB@5'-CAC...UUAUC U GU UG A AC CAUUU...ACU-3'@LB@ GG GGUGGUUU UGGU GGUUG CAU UGGGU@LB@ \|\| \|\|\|\|\|\|\|: \|\|\|\| :\|:\|: \|\|\| \|\|\|\|\|@LB@ CC CCACCAAG ACCA UCGAU GUA ACCCA@LB@3'-UUU...CGAUU U G UG C AAAU AUACA...UCG-5'@LB@ \| \|@LB@ 50 13@LB@@LB@@LB@Energy -20.16 kcal/mol@LB@Hybridization Energy -33.3931 kcal/mol@LB@Unfolding Energy - mRNA 8.66349 kcal/mol@LB@Unfolding Energy - sRNA 4.57395 kcal/mol@LB@@LB@Position - mRNA 81 -- 115@LB@Position - sRNA 14 -- 49@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 39 -- 45@LB@
62	0.00164	0.08891	b0922	mukF	-17.51	0.001582	1 -- 30	14 -- 38	chromosome condensin MukBEF kleisin-like subunit binds calcium	______________1_____________________________31\n______________\|_____________________________\|\n___________5'-____AAGAA__U________AA________AAGAC...UGG-3'\n______________CUGG_____GC_GGUUGGCA__UUAUGGGU\n______________\|\|\|\|_____:\|_:\|:\|:\|\|\|__\|\|\|\|\|\|\|\|\n______________GACC_____UG_UCGAUCGU__AAUACCCA\n3'-UUU...CCAAG____A_______________AA________AUACA...UCG-5'\n_____________\|______________________________\|\n_____________39_____________________________13\n	24 -- 30	14 -- 20	-25.2653 kcal/mol	3.2564 kcal/mol	4.5012 kcal/mol	1 31@LB@ \| \|@LB@ 5'- AAGAA U AA AAGAC...UGG-3'@LB@ CUGG GC GGUUGGCA UUAUGGGU@LB@ \|\|\|\| :\| :\|:\|:\|\|\| \|\|\|\|\|\|\|\|@LB@ GACC UG UCGAUCGU AAUACCCA@LB@3'-UUU...CCAAG A AA AUACA...UCG-5'@LB@ \| \|@LB@ 39 13@LB@@LB@@LB@Energy -17.51 kcal/mol@LB@Hybridization Energy -25.2653 kcal/mol@LB@Unfolding Energy - mRNA 3.2564 kcal/mol@LB@Unfolding Energy - sRNA 4.5012 kcal/mol@LB@@LB@Position - mRNA 1 -- 30@LB@Position - sRNA 14 -- 38@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 14 -- 20@LB@
66	0.001771	0.09017	b0924	mukB	-12.08	0.063147	4 -- 24	1 -- 22	chromosome condensin MukBEF ATPase and DNA-binding subunit	_____________3______________________25\n_____________\|______________________\|\n________5'-UGG________CCACGACAG_____AAGUU...CUG-3'\n______________UUUAUGGG__________CAGC\n______________\|\|\|\|\|\|\|\|__________\|\|\|\|\n______________AAAUACCC__________GUCG\n3'-UUU...UCGUA________AAUACAAAAA____-5'\n_____________\|_____________________\|\n_____________23____________________1\n	5 -- 11	15 -- 21	-14.8798 kcal/mol	1.84387 kcal/mol	0.958674 kcal/mol	3 25@LB@ \| \|@LB@ 5'-UGG CCACGACAG AAGUU...CUG-3'@LB@ UUUAUGGG CAGC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|@LB@ AAAUACCC GUCG@LB@3'-UUU...UCGUA AAUACAAAAA -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -12.08 kcal/mol@LB@Hybridization Energy -14.8798 kcal/mol@LB@Unfolding Energy - mRNA 1.84387 kcal/mol@LB@Unfolding Energy - sRNA 0.958674 kcal/mol@LB@@LB@Position - mRNA 4 -- 24@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 15 -- 21@LB@
102	0.003761	0.123	b0928	aspC	-10.71	0.122473	105 -- 118	20 -- 33	aspartate aminotransferase PLP-dependent	_____________104____________119\n_____________\|______________\|\n5'-CGU...CAAAA_____CU_______CAUCA...UUG-3'\n______________ACAGC__GCGUUUU\n______________\|\|\|\|\|__\|\|:\|\|\|\|\n______________UGUCG__CGUAAAA\n3'-UUU...GACCA_____AU_______UACCC...UCG-5'\n_____________\|______________\|\n_____________34_____________19\n	112 -- 118	20 -- 26	-14.5276 kcal/mol	2.38321 kcal/mol	1.43447 kcal/mol	104 119@LB@ \| \|@LB@5'-CGU...CAAAA CU CAUCA...UUG-3'@LB@ ACAGC GCGUUUU@LB@ \|\|\|\|\| \|\|:\|\|\|\|@LB@ UGUCG CGUAAAA@LB@3'-UUU...GACCA AU UACCC...UCG-5'@LB@ \| \|@LB@ 34 19@LB@@LB@@LB@Energy -10.71 kcal/mol@LB@Hybridization Energy -14.5276 kcal/mol@LB@Unfolding Energy - mRNA 2.38321 kcal/mol@LB@Unfolding Energy - sRNA 1.43447 kcal/mol@LB@@LB@Position - mRNA 105 -- 118@LB@Position - sRNA 20 -- 33@LB@Position Seed - mRNA 112 -- 118@LB@Position Seed - sRNA 20 -- 26@LB@
57	0.001403	0.08147	b0948	rlmL	-12.46	0.051711	286 -- 300	33 -- 47	23S rRNA m(2)G2445 and m(7)G2069 methyltransferases SAM-dependent	_____________285____________300\n_____________\|______________\|\n5'-GAC...AUGCC_________AG____-3'\n______________AGGUGGUUC__GGUG\n______________\|\|\|\|\|\|\|\|\|__\|\|\|:\n______________UCCACCAAG__CCAU\n3'-UUU...AUUCC_________GA____GUCGA...UCG-5'\n_____________\|_______________\|\n_____________48______________32\n	288 -- 294	39 -- 45	-21.3846 kcal/mol	5.67574 kcal/mol	3.25146 kcal/mol	285 300@LB@ \| \|@LB@5'-GAC...AUGCC AG -3'@LB@ AGGUGGUUC GGUG@LB@ \|\|\|\|\|\|\|\|\| \|\|\|:@LB@ UCCACCAAG CCAU@LB@3'-UUU...AUUCC GA GUCGA...UCG-5'@LB@ \| \|@LB@ 48 32@LB@@LB@@LB@Energy -12.46 kcal/mol@LB@Hybridization Energy -21.3846 kcal/mol@LB@Unfolding Energy - mRNA 5.67574 kcal/mol@LB@Unfolding Energy - sRNA 3.25146 kcal/mol@LB@@LB@Position - mRNA 286 -- 300@LB@Position - sRNA 33 -- 47@LB@Position Seed - mRNA 288 -- 294@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)

Job resubmission

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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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