Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
146	0.006661	0.1605	b4479	dgoR	-11.67	0.120911	94 -- 106	61 -- 74	D-galactonate catabolism operon transcriptional repressor		_____________93_____________107\n_____________\|______________\|\n5'-UUU...ACAUU______________ACGCG...AAC-3'\n______________AC_ACGCACGGCAA\n______________\|\|_\|\|:\|\|\|:\|\|\|\|\n______________UG_UGUGUGUCGUU\n3'-UUU...GUUUC__A___________AAGCA...GCA-5'\n_____________\|______________\|\n_____________75_____________60\n	100 -- 106	61 -- 67	-16.8512 kcal/mol	1.93692 kcal/mol	3.24589 kcal/mol	93 107@LB@ \| \|@LB@5'-UUU...ACAUU ACGCG...AAC-3'@LB@ AC ACGCACGGCAA@LB@ \|\| \|\|:\|\|\|:\|\|\|\|@LB@ UG UGUGUGUCGUU@LB@3'-UUU...GUUUC A AAGCA...GCA-5'@LB@ \| \|@LB@ 75 60@LB@@LB@@LB@Energy -11.67 kcal/mol@LB@Hybridization Energy -16.8512 kcal/mol@LB@Unfolding Energy - mRNA 1.93692 kcal/mol@LB@Unfolding Energy - sRNA 3.24589 kcal/mol@LB@@LB@Position - mRNA 94 -- 106@LB@Position - sRNA 61 -- 74@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 61 -- 67@LB@
114	0.005004	0.1545	b0025	ribF	-11.63	0.123109	210 -- 237	43 -- 71	bifunctional riboflavin kinase/FAD synthetase		_____________209___________________________238\n_____________\|_____________________________\|\n5'-UGG...AGCUG__________UACAUAAUC____GC____CCCCG...GCG-3'\n______________AUACGCGGCA__________UCA__CAGG\n______________\|:\|\|:\|:\|\|\|__________\|\|\|__\|\|\|\|\n______________UGUGUGUCGU__________AGU__GUCC\n3'-UUU...UCUGA__________UAAGCAACAA___GA____CCUAA...GCA-5'\n_____________\|_____________________________\|\n_____________72____________________________42\n	213 -- 219	62 -- 68	-21.1915 kcal/mol	5.23887 kcal/mol	4.32409 kcal/mol	209 238@LB@ \| \|@LB@5'-UGG...AGCUG UACAUAAUC GC CCCCG...GCG-3'@LB@ AUACGCGGCA UCA CAGG@LB@ \|:\|\|:\|:\|\|\| \|\|\| \|\|\|\|@LB@ UGUGUGUCGU AGU GUCC@LB@3'-UUU...UCUGA UAAGCAACAA GA CCUAA...GCA-5'@LB@ \| \|@LB@ 72 42@LB@@LB@@LB@Energy -11.63 kcal/mol@LB@Hybridization Energy -21.1915 kcal/mol@LB@Unfolding Energy - mRNA 5.23887 kcal/mol@LB@Unfolding Energy - sRNA 4.32409 kcal/mol@LB@@LB@Position - mRNA 210 -- 237@LB@Position - sRNA 43 -- 71@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 62 -- 68@LB@
179	0.009001	0.1747	b2725	hycA	-11.58	0.125812	239 -- 264	43 -- 70	regulator of the transcriptional regulator FhlA		_____________238_____________________________265\n_____________\|_______________________________\|\n5'-UUA...UACAU__________CA____________CUA____ACCAG...AGG-3'\n______________CGCACAGCGG__UCG_____UCGC___CAGG\n______________\|:\|\|\|\|\|\|::__\|\|\|_____\|\|:\|___\|\|\|\|\n______________GUGUGUCGUU__AGC_____AGUG___GUCC\n3'-UUU...CUGAU__________A____AACAA____A______CCUAA...GCA-5'\n_____________\|_______________________________\|\n_____________71______________________________42\n	242 -- 248	61 -- 67	-23.0547 kcal/mol	7.15003 kcal/mol	4.32399 kcal/mol	238 265@LB@ \| \|@LB@5'-UUA...UACAU CA CUA ACCAG...AGG-3'@LB@ CGCACAGCGG UCG UCGC CAGG@LB@ \|:\|\|\|\|\|\|:: \|\|\| \|\|:\| \|\|\|\|@LB@ GUGUGUCGUU AGC AGUG GUCC@LB@3'-UUU...CUGAU A AACAA A CCUAA...GCA-5'@LB@ \| \|@LB@ 71 42@LB@@LB@@LB@Energy -11.58 kcal/mol@LB@Hybridization Energy -23.0547 kcal/mol@LB@Unfolding Energy - mRNA 7.15003 kcal/mol@LB@Unfolding Energy - sRNA 4.32399 kcal/mol@LB@@LB@Position - mRNA 239 -- 264@LB@Position - sRNA 43 -- 70@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 61 -- 67@LB@
52	0.001789	0.121	b1799	dmlR	-11.56	0.127346	72 -- 108	34 -- 68	transcriptional activator of dmlA	b3060	_____________71_______________________________________109\n_____________\|________________________________________\|\n5'-CGC...GGGAU_________ACGCA_______________UU_____C___CUUCC...CGG-3'\n______________CGCAGCAAU_____UCGU__UUUCA_UCA__GGGUU_UCA\n______________\|:\|\|\|\|\|\|\|_____\|\|\|\|__\|\|\|\|\|_\|\|\|__\|\|:\|\|_:\|\|\n______________GUGUCGUUA_____AGCA__AAAGU_AGU__CCUAA_GGU\n3'-UUU...GAUGU__________________AC_____G___CC_____A___ACGAA...GCA-5'\n_____________\|________________________________________\|\n_____________69_______________________________________33\n	74 -- 80	60 -- 66	-24.8584 kcal/mol	8.52016 kcal/mol	4.78423 kcal/mol	71 109@LB@ \| \|@LB@5'-CGC...GGGAU ACGCA UU C CUUCC...CGG-3'@LB@ CGCAGCAAU UCGU UUUCA UCA GGGUU UCA@LB@ \|:\|\|\|\|\|\|\| \|\|\|\| \|\|\|\|\| \|\|\| \|\|:\|\| :\|\|@LB@ GUGUCGUUA AGCA AAAGU AGU CCUAA GGU@LB@3'-UUU...GAUGU AC G CC A ACGAA...GCA-5'@LB@ \| \|@LB@ 69 33@LB@@LB@@LB@Energy -11.56 kcal/mol@LB@Hybridization Energy -24.8584 kcal/mol@LB@Unfolding Energy - mRNA 8.52016 kcal/mol@LB@Unfolding Energy - sRNA 4.78423 kcal/mol@LB@@LB@Position - mRNA 72 -- 108@LB@Position - sRNA 34 -- 68@LB@Position Seed - mRNA 74 -- 80@LB@Position Seed - sRNA 60 -- 66@LB@
8	3.984e-05	0.01752	b2752	cysD	-11.53	0.128779	103 -- 132	45 -- 74	sulfate adenylyltransferase subunit 2		_____________102____________________________133\n_____________\|______________________________\|\n5'-GCC...AAGGA_____U___UC_____G__AA_________UUCUC...UCU-3'\n______________ACUAC_CAU__UAAUU_GU__UUUCAUUCG\n______________\|\|\|\|\|_\|\|:__:\|\|\|\|_\|\|__\|\|\|\|\|:\|\|:\n______________UGAUG_GUG__GUUAA_CA__AAAGUGAGU\n3'-UUU...GUUUC_____U___UC_____G__AC_________CCCCU...GCA-5'\n_____________\|______________________________\|\n_____________75_____________________________44\n	126 -- 132	45 -- 51	-20.8412 kcal/mol	5.57115 kcal/mol	3.74056 kcal/mol	102 133@LB@ \| \|@LB@5'-GCC...AAGGA U UC G AA UUCUC...UCU-3'@LB@ ACUAC CAU UAAUU GU UUUCAUUCG@LB@ \|\|\|\|\| \|\|: :\|\|\|\| \|\| \|\|\|\|\|:\|\|:@LB@ UGAUG GUG GUUAA CA AAAGUGAGU@LB@3'-UUU...GUUUC U UC G AC CCCCU...GCA-5'@LB@ \| \|@LB@ 75 44@LB@@LB@@LB@Energy -11.53 kcal/mol@LB@Hybridization Energy -20.8412 kcal/mol@LB@Unfolding Energy - mRNA 5.57115 kcal/mol@LB@Unfolding Energy - sRNA 3.74056 kcal/mol@LB@@LB@Position - mRNA 103 -- 132@LB@Position - sRNA 45 -- 74@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 45 -- 51@LB@
65	0.002677	0.1417	b0584	fepA	-11.47	0.132508	209 -- 249	37 -- 78	ferrienterobactin outer membrane transporter		_____________208___________________________________________250\n_____________\|_____________________________________________\|\n5'-GAA...AACAA___________U_CCU___C________G____A__U________AUGGG...ACG-3'\n______________GAAGAUU_CAU_C___GGC___UUGUUG__UCA_UC_GGGGAUUU\n______________:\|\|\|\|:\|_\|\|:_\|___:\|\|___\|:\|\|\|\|__\|\|\|_\|\|_\|\|\|\|\|\|\|\|\n______________UUUCUGA_GUG_G___UCG___AGCAAC__AGU_AG_CCCCUAAA\n3'-UUU...ACCCG_______U___U_______UUA______AA___G__U________GGUAC...GCA-5'\n_____________\|_____________________________________________\|\n_____________79____________________________________________36\n	243 -- 249	37 -- 43	-30.6633 kcal/mol	14.4176 kcal/mol	4.77973 kcal/mol	208 250@LB@ \| \|@LB@5'-GAA...AACAA U CCU C G A U AUGGG...ACG-3'@LB@ GAAGAUU CAU C GGC UUGUUG UCA UC GGGGAUUU@LB@ :\|\|\|\|:\| \|\|: \| :\|\| \|:\|\|\|\| \|\|\| \|\| \|\|\|\|\|\|\|\|@LB@ UUUCUGA GUG G UCG AGCAAC AGU AG CCCCUAAA@LB@3'-UUU...ACCCG U U UUA AA G U GGUAC...GCA-5'@LB@ \| \|@LB@ 79 36@LB@@LB@@LB@Energy -11.47 kcal/mol@LB@Hybridization Energy -30.6633 kcal/mol@LB@Unfolding Energy - mRNA 14.4176 kcal/mol@LB@Unfolding Energy - sRNA 4.77973 kcal/mol@LB@@LB@Position - mRNA 209 -- 249@LB@Position - sRNA 37 -- 78@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 37 -- 43@LB@
35	0.0005607	0.05638	b1434	ydcN	-11.45	0.133710	242 -- 253	62 -- 74	putative DNA-binding transcriptional regulator	b1508 b1299	_____________241___________254\n_____________\|_____________\|\n5'-CGG...AAACA_____________GCGCG...CUA-3'\n______________ACUACGC_CAGCA\n______________\|\|\|\|\|:\|_\|\|\|\|\|\n______________UGAUGUG_GUCGU\n3'-UUU...GUUUC_______U_____UAAGC...GCA-5'\n_____________\|_____________\|\n_____________75____________61\n	242 -- 248	68 -- 74	-17.054 kcal/mol	2.36402 kcal/mol	3.24359 kcal/mol	241 254@LB@ \| \|@LB@5'-CGG...AAACA GCGCG...CUA-3'@LB@ ACUACGC CAGCA@LB@ \|\|\|\|\|:\| \|\|\|\|\|@LB@ UGAUGUG GUCGU@LB@3'-UUU...GUUUC U UAAGC...GCA-5'@LB@ \| \|@LB@ 75 61@LB@@LB@@LB@Energy -11.45 kcal/mol@LB@Hybridization Energy -17.054 kcal/mol@LB@Unfolding Energy - mRNA 2.36402 kcal/mol@LB@Unfolding Energy - sRNA 3.24359 kcal/mol@LB@@LB@Position - mRNA 242 -- 253@LB@Position - sRNA 62 -- 74@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 68 -- 74@LB@
42	0.0009586	0.08031	b3747	kup	-11.44	0.134185	159 -- 185	49 -- 77	potassium transporter		_____________158___________________________186\n_____________\|_____________________________\|\n5'-AAA...GCCAA_______A________U___AUA______ACGAA...GUG-3'\n______________GGGACUA_GCACA_CA_UUC____UUUCA\n______________::\|\|\|\|\|_:\|\|\|\|_\|\|_\|\|\|____\|\|\|\|\|\n______________UUCUGAU_UGUGU_GU_AAG____AAAGU\n3'-UUU...CCCGU_______G_____C__U___CAAC_____GAGUC...GCA-5'\n_____________\|_____________________________\|\n_____________78____________________________48\n	159 -- 165	71 -- 77	-19.3471 kcal/mol	4.22429 kcal/mol	3.68465 kcal/mol	158 186@LB@ \| \|@LB@5'-AAA...GCCAA A U AUA ACGAA...GUG-3'@LB@ GGGACUA GCACA CA UUC UUUCA@LB@ ::\|\|\|\|\| :\|\|\|\| \|\| \|\|\| \|\|\|\|\|@LB@ UUCUGAU UGUGU GU AAG AAAGU@LB@3'-UUU...CCCGU G C U CAAC GAGUC...GCA-5'@LB@ \| \|@LB@ 78 48@LB@@LB@@LB@Energy -11.44 kcal/mol@LB@Hybridization Energy -19.3471 kcal/mol@LB@Unfolding Energy - mRNA 4.22429 kcal/mol@LB@Unfolding Energy - sRNA 3.68465 kcal/mol@LB@@LB@Position - mRNA 159 -- 185@LB@Position - sRNA 49 -- 77@LB@Position Seed - mRNA 159 -- 165@LB@Position Seed - sRNA 71 -- 77@LB@
53	0.001859	0.1218	b0529	folD	-11.41	0.136116	200 -- 226	61 -- 85	bifunctional 5 10-methylene-tetrahydrofolate dehydrogenase/ 5 10-methylene-tetrahydrofolate cyclohydrolase		_____________199_________________________227\n_____________\|___________________________\|\n5'-CAA...UCUCU_____CA___________UG_______AACGA...CAC-3'\n______________GAUGG__GCAAAGAUUAU__ACGGUAA\n______________\|\|\|\|\|__\|\|\|\|\|\|\|:\|\|:__\|\|:\|:\|\|\n______________CUACC__CGUUUCUGAUG__UGUCGUU\n3'-UUU...ACCCU__________________UG_______AAGCA...GCA-5'\n_____________\|___________________________\|\n_____________86__________________________60\n	220 -- 226	61 -- 67	-27.4215 kcal/mol	5.77154 kcal/mol	10.2439 kcal/mol	199 227@LB@ \| \|@LB@5'-CAA...UCUCU CA UG AACGA...CAC-3'@LB@ GAUGG GCAAAGAUUAU ACGGUAA@LB@ \|\|\|\|\| \|\|\|\|\|\|\|:\|\|: \|\|:\|:\|\|@LB@ CUACC CGUUUCUGAUG UGUCGUU@LB@3'-UUU...ACCCU UG AAGCA...GCA-5'@LB@ \| \|@LB@ 86 60@LB@@LB@@LB@Energy -11.41 kcal/mol@LB@Hybridization Energy -27.4215 kcal/mol@LB@Unfolding Energy - mRNA 5.77154 kcal/mol@LB@Unfolding Energy - sRNA 10.2439 kcal/mol@LB@@LB@Position - mRNA 200 -- 226@LB@Position - sRNA 61 -- 85@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 61 -- 67@LB@
176	0.008803	0.1747	b1242	ychE	-11.39	0.137124	41 -- 64	45 -- 75	UPF0056 family inner membrane protein		_____________40______________________________65\n_____________\|_______________________________\|\n5'-CAU...UUGGU____________________________A__ACUAG...GCA-3'\n______________GGCUACAU_UAGCA______UGUUUUGC_CA\n______________\|:\|\|\|\|\|:_:\|\|\|\|______\|\|\|\|\|::\|_\|\|\n______________CUGAUGUG_GUCGU______ACAAAGUG_GU\n3'-UUU...CGUUU________U_____UAAGCA________A__CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	55 -- 61	48 -- 54	-19.9041 kcal/mol	4.77357 kcal/mol	3.74078 kcal/mol	40 65@LB@ \| \|@LB@5'-CAU...UUGGU A ACUAG...GCA-3'@LB@ GGCUACAU UAGCA UGUUUUGC CA@LB@ \|:\|\|\|\|\|: :\|\|\|\| \|\|\|\|\|::\| \|\|@LB@ CUGAUGUG GUCGU ACAAAGUG GU@LB@3'-UUU...CGUUU U UAAGCA A CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -11.39 kcal/mol@LB@Hybridization Energy -19.9041 kcal/mol@LB@Unfolding Energy - mRNA 4.77357 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 41 -- 64@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 55 -- 61@LB@Position Seed - sRNA 48 -- 54@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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

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service.

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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