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
138	0.007886	0.2012	b3991	thiG	-13.21	0.033127	237 -- 259	64 -- 85	thiamine biosynthesis ThiGH complex subunit	_____________236______________________260\n_____________\|________________________\|\n5'-GCA...CACAU____UUA_________________CGCUU...CCG-3'\n______________CUGU___CCGGCA_CAGGGAAAUU\n______________\|\|\|:___\|\|::\|\|_\|\|\|\|\|\|\|\|\|:\n______________GACG___GGUUGU_GUCCCUUUAG\n3'-UUU...CUUAU____C________G__________AACCG...GUG-5'\n_____________\|________________________\|\n_____________86_______________________63\n	253 -- 259	64 -- 70	-25.8634 kcal/mol	5.26561 kcal/mol	7.38387 kcal/mol	236 260@LB@ \| \|@LB@5'-GCA...CACAU UUA CGCUU...CCG-3'@LB@ CUGU CCGGCA CAGGGAAAUU@LB@ \|\|\|: \|\|::\|\| \|\|\|\|\|\|\|\|\|:@LB@ GACG GGUUGU GUCCCUUUAG@LB@3'-UUU...CUUAU C G AACCG...GUG-5'@LB@ \| \|@LB@ 86 63@LB@@LB@@LB@Energy -13.21 kcal/mol@LB@Hybridization Energy -25.8634 kcal/mol@LB@Unfolding Energy - mRNA 5.26561 kcal/mol@LB@Unfolding Energy - sRNA 7.38387 kcal/mol@LB@@LB@Position - mRNA 237 -- 259@LB@Position - sRNA 64 -- 85@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 64 -- 70@LB@
46	0.002359	0.1727	b4139	aspA	-15.43	0.012067	239 -- 273	37 -- 76	aspartate ammonia-lyase	_____________238_______________________________________274\n_____________\|_________________________________________\|\n5'-GAU...UUGGG_____________CCA____A____________C_______UUCAC...ACU-3'\n______________UACCAGGGAAGUU___GCUG_UGCC______UA_UAUGGUG\n______________:\|\|\|\|\|\|\|\|\|:\|:___\|\|\|\|_:\|\|\|______\|\|_\|\|\|\|:\|\|\n______________GUGGUCCCUUUAG___CGAC_GCGG______AU_AUACUAC\n3'-UUU...CGGUU_____________AAC_________CAUUUA__A_______UCAAU...GUG-5'\n_____________\|_________________________________________\|\n_____________77________________________________________36\n	267 -- 273	37 -- 43	-35.8845 kcal/mol	11.095 kcal/mol	9.35931 kcal/mol	238 274@LB@ \| \|@LB@5'-GAU...UUGGG CCA A C UUCAC...ACU-3'@LB@ UACCAGGGAAGUU GCUG UGCC UA UAUGGUG@LB@ :\|\|\|\|\|\|\|\|\|:\|: \|\|\|\| :\|\|\| \|\| \|\|\|\|:\|\|@LB@ GUGGUCCCUUUAG CGAC GCGG AU AUACUAC@LB@3'-UUU...CGGUU AAC CAUUUA A UCAAU...GUG-5'@LB@ \| \|@LB@ 77 36@LB@@LB@@LB@Energy -15.43 kcal/mol@LB@Hybridization Energy -35.8845 kcal/mol@LB@Unfolding Energy - mRNA 11.095 kcal/mol@LB@Unfolding Energy - sRNA 9.35931 kcal/mol@LB@@LB@Position - mRNA 239 -- 273@LB@Position - sRNA 37 -- 76@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 37 -- 43@LB@
64	0.003238	0.1727	b2578	eamB	-8.70	0.240388	240 -- 262	70 -- 85	cysteine and O-acetylserine exporter	_____________239_____________________263\n_____________\|_______________________\|\n5'-GUC...ACACC___AUUAC____AU_________ACCGA...CGC-3'\n______________CUG_____CGCU__GACGCCAGG\n______________\|\|\|_____\|\|\|:__:\|\|:\|\|\|\|\|\n______________GAC_____GCGG__UUGUGGUCC\n3'-UUU...CUUAU_______________________CUUUA...GUG-5'\n_____________\|_______________________\|\n_____________86______________________69\n	256 -- 262	70 -- 76	-20.6717 kcal/mol	4.69447 kcal/mol	7.27689 kcal/mol	239 263@LB@ \| \|@LB@5'-GUC...ACACC AUUAC AU ACCGA...CGC-3'@LB@ CUG CGCU GACGCCAGG@LB@ \|\|\| \|\|\|: :\|\|:\|\|\|\|\|@LB@ GAC GCGG UUGUGGUCC@LB@3'-UUU...CUUAU CUUUA...GUG-5'@LB@ \| \|@LB@ 86 69@LB@@LB@@LB@Energy -8.70 kcal/mol@LB@Hybridization Energy -20.6717 kcal/mol@LB@Unfolding Energy - mRNA 4.69447 kcal/mol@LB@Unfolding Energy - sRNA 7.27689 kcal/mol@LB@@LB@Position - mRNA 240 -- 262@LB@Position - sRNA 70 -- 85@LB@Position Seed - mRNA 256 -- 262@LB@Position Seed - sRNA 70 -- 76@LB@
79	0.004357	0.1855	b0008	talB	-10.61	0.106795	240 -- 280	50 -- 88	transaldolase B	_____________239________________________________________281\n_____________\|__________________________________________\|\n5'-AGG...CCACC___G_________________C___GC___AAUGAA______UCAAC...CAA-3'\n______________GUA_UG_GCCGACACUGGGGA_AUC__GGC______GCUGUA\n______________:\|\|_\|\|_\|\|\|:\|\|\|\|::\|\|\|\|_\|\|\|__\|\|\|______\|\|:\|\|\|\n______________UAU_AC_CGGUUGUGGUCCCU_UAG__CCG______CGGCAU\n3'-UUU...GCGCU___G__G______________U___AA___ACG_________UUAAU...GUG-5'\n_____________\|__________________________________________\|\n_____________89_________________________________________49\n	253 -- 259	68 -- 74	-44.9099 kcal/mol	17.4497 kcal/mol	16.8544 kcal/mol	239 281@LB@ \| \|@LB@5'-AGG...CCACC G C GC AAUGAA UCAAC...CAA-3'@LB@ GUA UG GCCGACACUGGGGA AUC GGC GCUGUA@LB@ :\|\| \|\| \|\|\|:\|\|\|\|::\|\|\|\| \|\|\| \|\|\| \|\|:\|\|\|@LB@ UAU AC CGGUUGUGGUCCCU UAG CCG CGGCAU@LB@3'-UUU...GCGCU G G U AA ACG UUAAU...GUG-5'@LB@ \| \|@LB@ 89 49@LB@@LB@@LB@Energy -10.61 kcal/mol@LB@Hybridization Energy -44.9099 kcal/mol@LB@Unfolding Energy - mRNA 17.4497 kcal/mol@LB@Unfolding Energy - sRNA 16.8544 kcal/mol@LB@@LB@Position - mRNA 240 -- 280@LB@Position - sRNA 50 -- 88@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 68 -- 74@LB@
81	0.004478	0.1855	b3327	gspF	-8.77	0.233220	243 -- 251	26 -- 34	general secretory pathway component cryptic	_____________242_______252\n_____________\|_________\|\n5'-AUG...AAAAA_________AUCAU...AAG-3'\n______________UUGCAAGGG\n______________\|\|:\|\|\|\|\|\|\n______________AAUGUUCCC\n3'-UUU...UACUC_________GUGUC...GUG-5'\n_____________\|_________\|\n_____________35________25\n	245 -- 251	26 -- 32	-12.3281 kcal/mol	0.874927 kcal/mol	2.67841 kcal/mol	242 252@LB@ \| \|@LB@5'-AUG...AAAAA AUCAU...AAG-3'@LB@ UUGCAAGGG@LB@ \|\|:\|\|\|\|\|\|@LB@ AAUGUUCCC@LB@3'-UUU...UACUC GUGUC...GUG-5'@LB@ \| \|@LB@ 35 25@LB@@LB@@LB@Energy -8.77 kcal/mol@LB@Hybridization Energy -12.3281 kcal/mol@LB@Unfolding Energy - mRNA 0.874927 kcal/mol@LB@Unfolding Energy - sRNA 2.67841 kcal/mol@LB@@LB@Position - mRNA 243 -- 251@LB@Position - sRNA 26 -- 34@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 26 -- 32@LB@
27	0.001577	0.1727	b1679	sufE	-9.94	0.142549	247 -- 262	68 -- 86	sulfur acceptor protein	_____________246_________________263\n_____________\|___________________\|\n5'-AUG...UUUAC___________U_______AGAGA...GUC-3'\n______________GCUGCGCCAAC____GGGA\n______________:\|\|\|\|\|\|\|\|\|\|____\|\|\|\|\n______________UGACGCGGUUG____CCCU\n3'-UUU...GCUUA___________UGGU____UUAGA...GUG-5'\n_____________\|___________________\|\n_____________87__________________67\n	251 -- 257	76 -- 82	-25.4399 kcal/mol	8.12138 kcal/mol	7.37523 kcal/mol	246 263@LB@ \| \|@LB@5'-AUG...UUUAC U AGAGA...GUC-3'@LB@ GCUGCGCCAAC GGGA@LB@ :\|\|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UGACGCGGUUG CCCU@LB@3'-UUU...GCUUA UGGU UUAGA...GUG-5'@LB@ \| \|@LB@ 87 67@LB@@LB@@LB@Energy -9.94 kcal/mol@LB@Hybridization Energy -25.4399 kcal/mol@LB@Unfolding Energy - mRNA 8.12138 kcal/mol@LB@Unfolding Energy - sRNA 7.37523 kcal/mol@LB@@LB@Position - mRNA 247 -- 262@LB@Position - sRNA 68 -- 86@LB@Position Seed - mRNA 251 -- 257@LB@Position Seed - sRNA 76 -- 82@LB@
36	0.001988	0.1727	b2573	rpoE	-9.66	0.161217	247 -- 255	64 -- 72	RNA polymerase sigma E factor	_____________246_______256\n_____________\|_________\|\n5'-ACA...CCAGA_________AGAAA...UGG-3'\n______________AGGGAGAUC\n______________\|\|\|\|\|:\|\|\|\n______________UCCCUUUAG\n3'-UUU...UGUGG_________AACCG...GUG-5'\n_____________\|_________\|\n_____________73________63\n	249 -- 255	64 -- 70	-13.5601 kcal/mol	1.40253 kcal/mol	2.50058 kcal/mol	246 256@LB@ \| \|@LB@5'-ACA...CCAGA AGAAA...UGG-3'@LB@ AGGGAGAUC@LB@ \|\|\|\|\|:\|\|\|@LB@ UCCCUUUAG@LB@3'-UUU...UGUGG AACCG...GUG-5'@LB@ \| \|@LB@ 73 63@LB@@LB@@LB@Energy -9.66 kcal/mol@LB@Hybridization Energy -13.5601 kcal/mol@LB@Unfolding Energy - mRNA 1.40253 kcal/mol@LB@Unfolding Energy - sRNA 2.50058 kcal/mol@LB@@LB@Position - mRNA 247 -- 255@LB@Position - sRNA 64 -- 72@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 64 -- 70@LB@
70	0.003478	0.1727	b1919	dcyD	-7.16	0.432573	249 -- 279	53 -- 83	D-cysteine desulfhydrase PLP-dependent	_____________248_______________________________280\n_____________\|_________________________________\|\n5'-CUG...UCGGC____________CUC___U________C_____UUUCU...GGG-3'\n______________GCGCCAACGCCG___GAA_AUCU__GC_GCGCU\n______________\|\|\|\|\|\|\|\|:\|\|:___\|\|\|_\|\|\|\|__\|\|_\|\|\|\|:\n______________CGCGGUUGUGGU___CUU_UAGA__CG_CGCGG\n3'-UUU...UAUGA____________CC_________AC__A_____CAUUU...GUG-5'\n_____________\|_________________________________\|\n_____________84________________________________52\n	252 -- 258	74 -- 80	-36.5845 kcal/mol	12.956 kcal/mol	16.4685 kcal/mol	248 280@LB@ \| \|@LB@5'-CUG...UCGGC CUC U C UUUCU...GGG-3'@LB@ GCGCCAACGCCG GAA AUCU GC GCGCU@LB@ \|\|\|\|\|\|\|\|:\|\|: \|\|\| \|\|\|\| \|\| \|\|\|\|:@LB@ CGCGGUUGUGGU CUU UAGA CG CGCGG@LB@3'-UUU...UAUGA CC AC A CAUUU...GUG-5'@LB@ \| \|@LB@ 84 52@LB@@LB@@LB@Energy -7.16 kcal/mol@LB@Hybridization Energy -36.5845 kcal/mol@LB@Unfolding Energy - mRNA 12.956 kcal/mol@LB@Unfolding Energy - sRNA 16.4685 kcal/mol@LB@@LB@Position - mRNA 249 -- 279@LB@Position - sRNA 53 -- 83@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 74 -- 80@LB@
48	0.002388	0.1727	b2198	ccmD	-12.59	0.043972	250 -- 282	36 -- 77	cytochrome c biogenesis protein; heme export ABC transporter holo-CcmE release factor	_____________249________________________________________283\n_____________\|__________________________________________\|\n5'-UGG...CGGUU_____UUUUUU_____________G_________________CCGUU...UGG-3'\n______________ACGCC______GUC_UGGCUG_GC_GUG_______GUGAUGA\n______________\|\|:\|\|______:\|\|_\|\|\|\|\|\|_\|\|_\|\|:_______:\|\|\|\|\|\|\n______________UGUGG______UAG_ACCGAC_CG_CAU_______UACUACU\n3'-UUU...GCGGU_____UCCCUU___A______G__G___UUAAUAA_______CAAUG...GUG-5'\n_____________\|__________________________________________\|\n_____________78_________________________________________35\n	276 -- 282	36 -- 42	-31.2682 kcal/mol	9.31707 kcal/mol	9.36195 kcal/mol	249 283@LB@ \| \|@LB@5'-UGG...CGGUU UUUUUU G CCGUU...UGG-3'@LB@ ACGCC GUC UGGCUG GC GUG GUGAUGA@LB@ \|\|:\|\| :\|\| \|\|\|\|\|\| \|\| \|\|: :\|\|\|\|\|\|@LB@ UGUGG UAG ACCGAC CG CAU UACUACU@LB@3'-UUU...GCGGU UCCCUU A G G UUAAUAA CAAUG...GUG-5'@LB@ \| \|@LB@ 78 35@LB@@LB@@LB@Energy -12.59 kcal/mol@LB@Hybridization Energy -31.2682 kcal/mol@LB@Unfolding Energy - mRNA 9.31707 kcal/mol@LB@Unfolding Energy - sRNA 9.36195 kcal/mol@LB@@LB@Position - mRNA 250 -- 282@LB@Position - sRNA 36 -- 77@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 36 -- 42@LB@
107	0.005754	0.1855	b3447	ggt	-8.41	0.270031	252 -- 270	52 -- 70	gamma-glutamyltranspeptidase	_____________251_________________271\n_____________\|___________________\|\n5'-GUU...UCUCA_______GUUUUA______CCGCC...CGU-3'\n______________GGAAGUU______GCGCCG\n______________\|\|\|\|:\|:______\|\|\|\|\|\|\n______________CCUUUAG______CGCGGC\n3'-UUU...UGGUC_______AACCGA______AUUUA...GUG-5'\n_____________\|___________________\|\n_____________71__________________51\n	252 -- 258	64 -- 70	-19.4063 kcal/mol	4.14766 kcal/mol	6.84683 kcal/mol	251 271@LB@ \| \|@LB@5'-GUU...UCUCA GUUUUA CCGCC...CGU-3'@LB@ GGAAGUU GCGCCG@LB@ \|\|\|\|:\|: \|\|\|\|\|\|@LB@ CCUUUAG CGCGGC@LB@3'-UUU...UGGUC AACCGA AUUUA...GUG-5'@LB@ \| \|@LB@ 71 51@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -19.4063 kcal/mol@LB@Unfolding Energy - mRNA 4.14766 kcal/mol@LB@Unfolding Energy - sRNA 6.84683 kcal/mol@LB@@LB@Position - mRNA 252 -- 270@LB@Position - sRNA 52 -- 70@LB@Position Seed - mRNA 252 -- 258@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)

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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