Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
23	0.001421	0.1727	b1234	rssA	-12.55	0.044848	179 -- 192	61 -- 74	putative patatin-like family phospholipase		_____________178____________193\n_____________\|______________\|\n5'-GAU...GCAUU______________CGGGA...AAA-3'\n______________CCAGGGGAAUCUUG\n______________\|\|\|\|\|\|:\|\|\|\|\|\|\|\n______________GGUCCCUUUAGAAC\n3'-UUU...GUUGU______________CGACG...GUG-5'\n_____________\|______________\|\n_____________75_____________60\n	186 -- 192	61 -- 67	-22.3239 kcal/mol	6.14875 kcal/mol	3.62869 kcal/mol	178 193@LB@ \| \|@LB@5'-GAU...GCAUU CGGGA...AAA-3'@LB@ CCAGGGGAAUCUUG@LB@ \|\|\|\|\|\|:\|\|\|\|\|\|\|@LB@ GGUCCCUUUAGAAC@LB@3'-UUU...GUUGU CGACG...GUG-5'@LB@ \| \|@LB@ 75 60@LB@@LB@@LB@Energy -12.55 kcal/mol@LB@Hybridization Energy -22.3239 kcal/mol@LB@Unfolding Energy - mRNA 6.14875 kcal/mol@LB@Unfolding Energy - sRNA 3.62869 kcal/mol@LB@@LB@Position - mRNA 179 -- 192@LB@Position - sRNA 61 -- 74@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 61 -- 67@LB@
90	0.004828	0.1855	b2149	mglA	-7.32	0.409352	216 -- 239	61 -- 86	methyl-galactoside ABC transporter ATPase		_____________215________________________240\n_____________\|__________________________\|\n5'-CGA...CAACG___C____CU__________UA____UUGGA...AUU-3'\n______________ACU_CGUC____CCGGGGAA__CUUG\n______________\|\|\|_\|\|:\|____\|\|:\|\|\|\|\|__\|\|\|\|\n______________UGA_GCGG____GGUCCCUU__GAAC\n3'-UUU...GCUUA___C____UUGU________UA____CGACG...GUG-5'\n_____________\|__________________________\|\n_____________87_________________________60\n	227 -- 233	67 -- 73	-23.5814 kcal/mol	8.829 kcal/mol	7.43637 kcal/mol	215 240@LB@ \| \|@LB@5'-CGA...CAACG C CU UA UUGGA...AUU-3'@LB@ ACU CGUC CCGGGGAA CUUG@LB@ \|\|\| \|\|:\| \|\|:\|\|\|\|\| \|\|\|\|@LB@ UGA GCGG GGUCCCUU GAAC@LB@3'-UUU...GCUUA C UUGU UA CGACG...GUG-5'@LB@ \| \|@LB@ 87 60@LB@@LB@@LB@Energy -7.32 kcal/mol@LB@Hybridization Energy -23.5814 kcal/mol@LB@Unfolding Energy - mRNA 8.829 kcal/mol@LB@Unfolding Energy - sRNA 7.43637 kcal/mol@LB@@LB@Position - mRNA 216 -- 239@LB@Position - sRNA 61 -- 86@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 67 -- 73@LB@
21	0.001192	0.1727	b2526	hscA	-14.48	0.018641	235 -- 259	63 -- 88	DnaK-like molecular chaperone specific for IscU		_____________234________________________260\n_____________\|__________________________\|\n5'-AGC...UUUGA__________________C_UC____GGCGG...UGG-3'\n______________GUGCUGCGCC_GCAUCAG_G__GUCU\n______________:\|:\|\|\|\|\|\|\|_:\|\|:\|\|\|_\|__:\|\|\|\n______________UAUGACGCGG_UGUGGUC_C__UAGA\n3'-UUU...GCGCU__________U_______C_UU____ACCGA...GUG-5'\n_____________\|__________________________\|\n_____________89_________________________62\n	245 -- 251	71 -- 77	-31.0682 kcal/mol	9.20475 kcal/mol	7.38674 kcal/mol	234 260@LB@ \| \|@LB@5'-AGC...UUUGA C UC GGCGG...UGG-3'@LB@ GUGCUGCGCC GCAUCAG G GUCU@LB@ :\|:\|\|\|\|\|\|\| :\|\|:\|\|\| \| :\|\|\|@LB@ UAUGACGCGG UGUGGUC C UAGA@LB@3'-UUU...GCGCU U C UU ACCGA...GUG-5'@LB@ \| \|@LB@ 89 62@LB@@LB@@LB@Energy -14.48 kcal/mol@LB@Hybridization Energy -31.0682 kcal/mol@LB@Unfolding Energy - mRNA 9.20475 kcal/mol@LB@Unfolding Energy - sRNA 7.38674 kcal/mol@LB@@LB@Position - mRNA 235 -- 259@LB@Position - sRNA 63 -- 88@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 71 -- 77@LB@
30	0.001614	0.1727	b3607	cysE	-13.31	0.031682	13 -- 32	63 -- 81	serine acetyltransferase		_____________12___________________33\n_____________\|____________________\|\n5'-CGG...GAAAU______A____A________AUCAA...CGA-3'\n______________GCCAAU_ACCG_GGAAAUUU\n______________\|\|\|\|\|:_\|\|\|:_\|\|\|\|\|\|:\|\n______________CGGUUG_UGGU_CCUUUAGA\n3'-UUU...UGACG___________C________ACCGA...GUG-5'\n_____________\|____________________\|\n_____________82___________________62\n	26 -- 32	63 -- 69	-21.8966 kcal/mol	1.53041 kcal/mol	7.0543 kcal/mol	12 33@LB@ \| \|@LB@5'-CGG...GAAAU A A AUCAA...CGA-3'@LB@ GCCAAU ACCG GGAAAUUU@LB@ \|\|\|\|\|: \|\|\|: \|\|\|\|\|\|:\|@LB@ CGGUUG UGGU CCUUUAGA@LB@3'-UUU...UGACG C ACCGA...GUG-5'@LB@ \| \|@LB@ 82 62@LB@@LB@@LB@Energy -13.31 kcal/mol@LB@Hybridization Energy -21.8966 kcal/mol@LB@Unfolding Energy - mRNA 1.53041 kcal/mol@LB@Unfolding Energy - sRNA 7.0543 kcal/mol@LB@@LB@Position - mRNA 13 -- 32@LB@Position - sRNA 63 -- 81@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 63 -- 69@LB@
88	0.004799	0.1855	b2213	ada	-9.32	0.185618	222 -- 245	63 -- 86	fused DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase		_____________221________________________246\n_____________\|__________________________\|\n5'-GGA...GCUUA____A__A__________C_______GUCUU...CCA-3'\n______________ACUG_CG_UCAACGCUGG___AAUCU\n______________\|\|\|\|_\|\|_:\|\|\|\|:\|::\|___\|\|\|\|\|\n______________UGAC_GC_GGUUGUGGUC___UUAGA\n3'-UUU...GCUUA__________________CCU_____ACCGA...GUG-5'\n_____________\|__________________________\|\n_____________87_________________________62\n	233 -- 239	71 -- 77	-21.7615 kcal/mol	5.05104 kcal/mol	7.38602 kcal/mol	221 246@LB@ \| \|@LB@5'-GGA...GCUUA A A C GUCUU...CCA-3'@LB@ ACUG CG UCAACGCUGG AAUCU@LB@ \|\|\|\| \|\| :\|\|\|\|:\|::\| \|\|\|\|\|@LB@ UGAC GC GGUUGUGGUC UUAGA@LB@3'-UUU...GCUUA CCU ACCGA...GUG-5'@LB@ \| \|@LB@ 87 62@LB@@LB@@LB@Energy -9.32 kcal/mol@LB@Hybridization Energy -21.7615 kcal/mol@LB@Unfolding Energy - mRNA 5.05104 kcal/mol@LB@Unfolding Energy - sRNA 7.38602 kcal/mol@LB@@LB@Position - mRNA 222 -- 245@LB@Position - sRNA 63 -- 86@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 71 -- 77@LB@
108	0.005783	0.1855	b3951	pflD	-15.90	0.009733	233 -- 258	63 -- 86	putative glycine radical domain-containing pyruvate formate-lyase	b0823	_____________232________________________259\n_____________\|__________________________\|\n5'-GAU...ACUGC_____UU_________C_U_______CGCUG...AAA-3'\n______________ACUGU__GCCAAUACC_G_GAAAUCU\n______________\|\|\|\|:__\|\|\|\|\|:\|\|\|_\|_\|\|\|\|\|\|\|\n______________UGACG__CGGUUGUGG_C_CUUUAGA\n3'-UUU...GCUUA________________U_C_______ACCGA...GUG-5'\n_____________\|__________________________\|\n_____________87_________________________62\n	252 -- 258	63 -- 69	-27.9307 kcal/mol	4.64309 kcal/mol	7.38602 kcal/mol	232 259@LB@ \| \|@LB@5'-GAU...ACUGC UU C U CGCUG...AAA-3'@LB@ ACUGU GCCAAUACC G GAAAUCU@LB@ \|\|\|\|: \|\|\|\|\|:\|\|\| \| \|\|\|\|\|\|\|@LB@ UGACG CGGUUGUGG C CUUUAGA@LB@3'-UUU...GCUUA U C ACCGA...GUG-5'@LB@ \| \|@LB@ 87 62@LB@@LB@@LB@Energy -15.90 kcal/mol@LB@Hybridization Energy -27.9307 kcal/mol@LB@Unfolding Energy - mRNA 4.64309 kcal/mol@LB@Unfolding Energy - sRNA 7.38602 kcal/mol@LB@@LB@Position - mRNA 233 -- 258@LB@Position - sRNA 63 -- 86@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 63 -- 69@LB@
116	0.006112	0.1855	b1260	trpA	-12.39	0.048115	172 -- 199	63 -- 89	tryptophan synthase alpha subunit		_____________171__________________________200\n_____________\|____________________________\|\n5'-GCC...UUCAC______U__AA_____GA__________GAUGG...CAU-3'\n______________GAUAUU_UG__AGCAC__GGGGAAAUCU\n______________:\|\|\|:\|_:\|__\|:\|\|\|__:\|\|\|\|\|\|\|\|\|\n______________UUAUGA_GC__UUGUG__UCCCUUUAGA\n3'-UUU...CGCGC______C__GG_____G___________ACCGA...GUG-5'\n_____________\|____________________________\|\n_____________90___________________________62\n	193 -- 199	63 -- 69	-25.3377 kcal/mol	5.06327 kcal/mol	7.88429 kcal/mol	171 200@LB@ \| \|@LB@5'-GCC...UUCAC U AA GA GAUGG...CAU-3'@LB@ GAUAUU UG AGCAC GGGGAAAUCU@LB@ :\|\|\|:\| :\| \|:\|\|\| :\|\|\|\|\|\|\|\|\|@LB@ UUAUGA GC UUGUG UCCCUUUAGA@LB@3'-UUU...CGCGC C GG G ACCGA...GUG-5'@LB@ \| \|@LB@ 90 62@LB@@LB@@LB@Energy -12.39 kcal/mol@LB@Hybridization Energy -25.3377 kcal/mol@LB@Unfolding Energy - mRNA 5.06327 kcal/mol@LB@Unfolding Energy - sRNA 7.88429 kcal/mol@LB@@LB@Position - mRNA 172 -- 199@LB@Position - sRNA 63 -- 89@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 63 -- 69@LB@
131	0.007315	0.1966	b3824	rhtB	-9.48	0.174149	77 -- 100	63 -- 87	homoserine homoserine lactone and S-methyl-methionine efflux pump		_____________76________________________101\n_____________\|_________________________\|\n5'-ACG...CUUUU______UGA_________U______GCCUC...ACC-3'\n______________UGCUGC___AACAUCGGG__AAUCU\n______________\|:\|\|\|\|___\|\|\|\|:\|:\|\|__\|\|\|\|\|\n______________AUGACG___UUGUGGUCC__UUAGA\n3'-UUU...CGCUU______CGG_________CU_____ACCGA...GUG-5'\n_____________\|_________________________\|\n_____________88________________________62\n	88 -- 94	70 -- 76	-24.9255 kcal/mol	8.06413 kcal/mol	7.38606 kcal/mol	76 101@LB@ \| \|@LB@5'-ACG...CUUUU UGA U GCCUC...ACC-3'@LB@ UGCUGC AACAUCGGG AAUCU@LB@ \|:\|\|\|\| \|\|\|\|:\|:\|\| \|\|\|\|\|@LB@ AUGACG UUGUGGUCC UUAGA@LB@3'-UUU...CGCUU CGG CU ACCGA...GUG-5'@LB@ \| \|@LB@ 88 62@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -24.9255 kcal/mol@LB@Unfolding Energy - mRNA 8.06413 kcal/mol@LB@Unfolding Energy - sRNA 7.38606 kcal/mol@LB@@LB@Position - mRNA 77 -- 100@LB@Position - sRNA 63 -- 87@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 70 -- 76@LB@
151	0.008943	0.2059	b1284	yciT	-9.40	0.179701	94 -- 109	63 -- 77	global regulator of transcription; DeoR family		_____________93_______________110\n_____________\|________________\|\n5'-GCA...CGAAG______U_________AACAA...CCA-3'\n______________GCACCG_GGGAGAUUU\n______________:\|\|\|\|:_\|\|\|\|:\|\|:\|\n______________UGUGGU_CCCUUUAGA\n3'-UUU...GCGGU________________ACCGA...GUG-5'\n_____________\|________________\|\n_____________78_______________62\n	103 -- 109	63 -- 69	-19.5221 kcal/mol	5.38652 kcal/mol	4.72953 kcal/mol	93 110@LB@ \| \|@LB@5'-GCA...CGAAG U AACAA...CCA-3'@LB@ GCACCG GGGAGAUUU@LB@ :\|\|\|\|: \|\|\|\|:\|\|:\|@LB@ UGUGGU CCCUUUAGA@LB@3'-UUU...GCGGU ACCGA...GUG-5'@LB@ \| \|@LB@ 78 62@LB@@LB@@LB@Energy -9.40 kcal/mol@LB@Hybridization Energy -19.5221 kcal/mol@LB@Unfolding Energy - mRNA 5.38652 kcal/mol@LB@Unfolding Energy - sRNA 4.72953 kcal/mol@LB@@LB@Position - mRNA 94 -- 109@LB@Position - sRNA 63 -- 77@LB@Position Seed - mRNA 103 -- 109@LB@Position Seed - sRNA 63 -- 69@LB@
4	3.471e-06	0.003055	b2099	yegU	-19.38	0.001997	173 -- 198	64 -- 88	ADP-ribosylglycohydrolase family protein		_____________172________________________199\n_____________\|__________________________\|\n5'-GUG...UCGCG_______________AA_________AAAUG...CAC-3'\n______________AUAUUGCGUUGACAC__GGGGAAGUU\n______________\|\|\|:\|\|\|\|:::\|\|\|\|__:\|\|\|\|\|:\|:\n______________UAUGACGCGGUUGUG__UCCCUUUAG\n3'-UUU...GCGCU_______________G__________AACCG...GUG-5'\n_____________\|__________________________\|\n_____________89_________________________63\n	192 -- 198	64 -- 70	-32.1286 kcal/mol	5.35868 kcal/mol	7.38555 kcal/mol	172 199@LB@ \| \|@LB@5'-GUG...UCGCG AA AAAUG...CAC-3'@LB@ AUAUUGCGUUGACAC GGGGAAGUU@LB@ \|\|\|:\|\|\|\|:::\|\|\|\| :\|\|\|\|\|:\|:@LB@ UAUGACGCGGUUGUG UCCCUUUAG@LB@3'-UUU...GCGCU G AACCG...GUG-5'@LB@ \| \|@LB@ 89 63@LB@@LB@@LB@Energy -19.38 kcal/mol@LB@Hybridization Energy -32.1286 kcal/mol@LB@Unfolding Energy - mRNA 5.35868 kcal/mol@LB@Unfolding Energy - sRNA 7.38555 kcal/mol@LB@@LB@Position - mRNA 173 -- 198@LB@Position - sRNA 64 -- 88@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 64 -- 70@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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