Input and runtime details for job 2727377 (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 2727377 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:09 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:28 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:18:35 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:18:43 CET 2018
	Job Completed		@ Fri Feb 16 20:19:11 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=2727377&toolName=CopraRNA ( 30 days expiry )

Description of the job

RyhB

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
107	0.0112	0.3489	b3012	dkgA	-15.28	0.024842	250 -- 292	50 -- 87	2 5-diketo-D-gluconate reductase A	_____________249__________________________________________293\n_____________\|____________________________________________\|\n5'-CUG...GCCCC______G___G___GUC____AAGC________A__________CACCGCCA-3'\n______________AGCUGG_ACU_GGC___UGGC____AAGUAAUG__GGAAGUAAU\n______________\|\|\|::\|_\|\|:_\|\|\|___\|\|\|\|____\|\|\|\|\|\|\|:__\|\|\|\|\|:\|\|\|\n______________UCGGUC_UGG_CCG___ACCG____UUCAUUAU__CCUUCGUUA\n________3'-UUU______G___G__________A___________GA_________CACUC...GCG-5'\n_____________\|____________________________________________\|\n_____________88___________________________________________49\n	286 -- 292	50 -- 56	-41.0731 kcal/mol	11.2031 kcal/mol	14.5934 kcal/mol	249 293@LB@ \| \|@LB@5'-CUG...GCCCC G G GUC AAGC A CACCGCCA-3'@LB@ AGCUGG ACU GGC UGGC AAGUAAUG GGAAGUAAU@LB@ \|\|\|::\| \|\|: \|\|\| \|\|\|\| \|\|\|\|\|\|\|: \|\|\|\|\|:\|\|\|@LB@ UCGGUC UGG CCG ACCG UUCAUUAU CCUUCGUUA@LB@ 3'-UUU G G A GA CACUC...GCG-5'@LB@ \| \|@LB@ 88 49@LB@@LB@@LB@Energy -15.28 kcal/mol@LB@Hybridization Energy -41.0731 kcal/mol@LB@Unfolding Energy - mRNA 11.2031 kcal/mol@LB@Unfolding Energy - sRNA 14.5934 kcal/mol@LB@@LB@Position - mRNA 250 -- 292@LB@Position - sRNA 50 -- 87@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 50 -- 56@LB@
181	0.0223	0.4113	b3770	ilvE	-12.64	0.069830	250 -- 281	37 -- 61	branched-chain amino acid aminotransferase	_____________249______________________________282\n_____________\|________________________________\|\n5'-UUU...GGUUC_______AGAC____AG___CAU_________CACGC...GCA-3'\n______________GCUGGGA____GCGA__GUG___GUGAUGUCG\n______________:\|\|\|\|:\|____\|\|:\|__\|\|\|___\|::\|\|\|\|\|\|\n______________UGACCUU____CGUU__CAC___CGUUACAGC\n3'-UUU...CAUUA_______________A____U___________ACGAA...GCG-5'\n_____________\|________________________________\|\n_____________62_______________________________36\n	275 -- 281	37 -- 43	-25.0056 kcal/mol	9.06403 kcal/mol	3.30158 kcal/mol	249 282@LB@ \| \|@LB@5'-UUU...GGUUC AGAC AG CAU CACGC...GCA-3'@LB@ GCUGGGA GCGA GUG GUGAUGUCG@LB@ :\|\|\|\|:\| \|\|:\| \|\|\| \|::\|\|\|\|\|\|@LB@ UGACCUU CGUU CAC CGUUACAGC@LB@3'-UUU...CAUUA A U ACGAA...GCG-5'@LB@ \| \|@LB@ 62 36@LB@@LB@@LB@Energy -12.64 kcal/mol@LB@Hybridization Energy -25.0056 kcal/mol@LB@Unfolding Energy - mRNA 9.06403 kcal/mol@LB@Unfolding Energy - sRNA 3.30158 kcal/mol@LB@@LB@Position - mRNA 250 -- 281@LB@Position - sRNA 37 -- 61@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 37 -- 43@LB@
73	0.006758	0.3082	b0073	leuB	-14.41	0.035044	252 -- 295	42 -- 89	3-isopropylmalate dehydrogenase NAD(+)-dependent	_____________251_______________________________________________296\n_____________\|_________________________________________________\|\n5'-AAA...GUCCG_____G_UG____A__________A__________U__C_____C____CCGCU-3'\n______________GAAGU_A__ACCC_GGC__GCUGA__AGUGCUGGA_GC___GUG_GCAA\n______________:\|\|\|:_\|__\|\|\|\|_\|\|\|__\|\|\|:\|__\|:\|:\|\|\|\|\|_\|\|___\|\|\|_\|\|\|\|\n______________UUUCG_U__UGGG_CCG__CGAUU__UUAUGACCU_CG___CAC_CGUU\n__________3'-U_____G_CG________AC_____CA_________U__UUA___U____ACAGC...GCG-5'\n_____________\|_________________________________________________\|\n_____________90________________________________________________41\n	277 -- 283	56 -- 62	-44.364 kcal/mol	15.0484 kcal/mol	14.9103 kcal/mol	251 296@LB@ \| \|@LB@5'-AAA...GUCCG G UG A A U C C CCGCU-3'@LB@ GAAGU A ACCC GGC GCUGA AGUGCUGGA GC GUG GCAA@LB@ :\|\|\|: \| \|\|\|\| \|\|\| \|\|\|:\| \|:\|:\|\|\|\|\| \|\| \|\|\| \|\|\|\|@LB@ UUUCG U UGGG CCG CGAUU UUAUGACCU CG CAC CGUU@LB@ 3'-U G CG AC CA U UUA U ACAGC...GCG-5'@LB@ \| \|@LB@ 90 41@LB@@LB@@LB@Energy -14.41 kcal/mol@LB@Hybridization Energy -44.364 kcal/mol@LB@Unfolding Energy - mRNA 15.0484 kcal/mol@LB@Unfolding Energy - sRNA 14.9103 kcal/mol@LB@@LB@Position - mRNA 252 -- 295@LB@Position - sRNA 42 -- 89@LB@Position Seed - mRNA 277 -- 283@LB@Position Seed - sRNA 56 -- 62@LB@
160	0.02006	0.4072	b1205	ychH	-13.92	0.042333	252 -- 283	22 -- 60	DUF2583 family putative inner membrane protein	_____________251_____________________________________284\n_____________\|_______________________________________\|\n5'-CAA...UGGGU____U____________G_________G__G____A___AAUCC...UAC-3'\n______________CUGG_GGUAAUG___GU___GUCG_GC__U_GGGU_UUC\n______________\|\|\|\|_:\|:\|\|\|\|___\|:___\|\|\|\|_\|\|__\|_:\|\|\|_:\|\|\n______________GACC_UCGUUAC___CG___CAGC_CG__A_UCCA_GAG\n3'-UUU...AUUAU____U_______ACU__UUA____A__AA_G____A___GCGCU...GCG-5'\n_____________\|_______________________________________\|\n_____________61______________________________________21\n	257 -- 263	49 -- 55	-28.0186 kcal/mol	6.10632 kcal/mol	7.98777 kcal/mol	251 284@LB@ \| \|@LB@5'-CAA...UGGGU U G G G A AAUCC...UAC-3'@LB@ CUGG GGUAAUG GU GUCG GC U GGGU UUC@LB@ \|\|\|\| :\|:\|\|\|\| \|: \|\|\|\| \|\| \| :\|\|\| :\|\|@LB@ GACC UCGUUAC CG CAGC CG A UCCA GAG@LB@3'-UUU...AUUAU U ACU UUA A AA G A GCGCU...GCG-5'@LB@ \| \|@LB@ 61 21@LB@@LB@@LB@Energy -13.92 kcal/mol@LB@Hybridization Energy -28.0186 kcal/mol@LB@Unfolding Energy - mRNA 6.10632 kcal/mol@LB@Unfolding Energy - sRNA 7.98777 kcal/mol@LB@@LB@Position - mRNA 252 -- 283@LB@Position - sRNA 22 -- 60@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 49 -- 55@LB@
111	0.01184	0.3513	b0528	ybcJ	-13.49	0.050278	257 -- 272	44 -- 61	ribosome-associated protein; putative RNA-binding protein	_____________256________________273\n_____________\|__________________\|\n5'-AGG...CUGAA________GC________GAAAG...CGA-3'\n______________ACUGGAAG___UG_GAGC\n______________\|\|\|\|\|\|\|\|___\|\|_\|\|\|\|\n______________UGACCUUC___AC_CUCG\n3'-UUU...CAUUA________GUU__A____UUACA...GCG-5'\n_____________\|__________________\|\n_____________62_________________43\n	258 -- 264	54 -- 60	-19.8617 kcal/mol	3.07726 kcal/mol	3.29941 kcal/mol	256 273@LB@ \| \|@LB@5'-AGG...CUGAA GC GAAAG...CGA-3'@LB@ ACUGGAAG UG GAGC@LB@ \|\|\|\|\|\|\|\| \|\| \|\|\|\|@LB@ UGACCUUC AC CUCG@LB@3'-UUU...CAUUA GUU A UUACA...GCG-5'@LB@ \| \|@LB@ 62 43@LB@@LB@@LB@Energy -13.49 kcal/mol@LB@Hybridization Energy -19.8617 kcal/mol@LB@Unfolding Energy - mRNA 3.07726 kcal/mol@LB@Unfolding Energy - sRNA 3.29941 kcal/mol@LB@@LB@Position - mRNA 257 -- 272@LB@Position - sRNA 44 -- 61@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 54 -- 60@LB@
192	0.02457	0.4226	b2689	yqaA	-16.30	0.016522	258 -- 300	44 -- 85	COG1238 family inner membrane protein	_____________257_________________________________________300\n_____________\|___________________________________________\|\n5'-CAC...CUACA___U________AACUCCG____C_______U________U___-3'\n______________CUA_UACCCGGC_______AAGU_GUGCUGG_GGCAAUGU__GC\n______________\|:\|_:\|\|\|\|\|\|\|_______\|\|\|\|_:\|:\|\|\|\|_:\|\|\|\|\|\|\|__\|\|\n______________GGU_GUGGGCCG_______UUCA_UAUGACC_UCGUUACA__CG\n______3'-UUUUC___C________ACCGA______U_______U________CU__UUACA...GCG-5'\n_____________\|____________________________________________\|\n_____________86___________________________________________43\n	291 -- 297	48 -- 54	-43.3701 kcal/mol	12.1561 kcal/mol	14.9093 kcal/mol	257 300@LB@ \| \|@LB@5'-CAC...CUACA U AACUCCG C U U -3'@LB@ CUA UACCCGGC AAGU GUGCUGG GGCAAUGU GC@LB@ \|:\| :\|\|\|\|\|\|\| \|\|\|\| :\|:\|\|\|\| :\|\|\|\|\|\|\| \|\|@LB@ GGU GUGGGCCG UUCA UAUGACC UCGUUACA CG@LB@ 3'-UUUUC C ACCGA U U CU UUACA...GCG-5'@LB@ \| \|@LB@ 86 43@LB@@LB@@LB@Energy -16.30 kcal/mol@LB@Hybridization Energy -43.3701 kcal/mol@LB@Unfolding Energy - mRNA 12.1561 kcal/mol@LB@Unfolding Energy - sRNA 14.9093 kcal/mol@LB@@LB@Position - mRNA 258 -- 300@LB@Position - sRNA 44 -- 85@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 48 -- 54@LB@
66	0.005808	0.2905	b2016	yeeZ	-14.47	0.034156	261 -- 292	51 -- 85	putative epimerase	_____________260_________________________________293\n_____________\|___________________________________\|\n5'-ACC...CACUU_______GA____________C____C________AACCACAC-3'\n______________UCAGCGC__GGCUGGC_AAGU___AC_GGGAGUAA\n______________:\|\|\|\|:\|__\|\|\|\|\|\|\|_\|\|\|\|___\|\|_\|\|:\|\|:\|\|\n______________GGUCGUG__CCGACCG_UUCA___UG_CCUUCGUU\n______3'-UUUUC_______GG_______A____UUA__A________ACACU...GCG-5'\n_____________\|___________________________________\|\n_____________86__________________________________50\n	286 -- 292	51 -- 57	-40.5662 kcal/mol	11.5945 kcal/mol	14.5012 kcal/mol	260 293@LB@ \| \|@LB@5'-ACC...CACUU GA C C AACCACAC-3'@LB@ UCAGCGC GGCUGGC AAGU AC GGGAGUAA@LB@ :\|\|\|\|:\| \|\|\|\|\|\|\| \|\|\|\| \|\| \|\|:\|\|:\|\|@LB@ GGUCGUG CCGACCG UUCA UG CCUUCGUU@LB@ 3'-UUUUC GG A UUA A ACACU...GCG-5'@LB@ \| \|@LB@ 86 50@LB@@LB@@LB@Energy -14.47 kcal/mol@LB@Hybridization Energy -40.5662 kcal/mol@LB@Unfolding Energy - mRNA 11.5945 kcal/mol@LB@Unfolding Energy - sRNA 14.5012 kcal/mol@LB@@LB@Position - mRNA 261 -- 292@LB@Position - sRNA 51 -- 85@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 51 -- 57@LB@
124	0.01356	0.3627	b2232	ubiG	-16.56	0.014945	261 -- 300	44 -- 89	bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase	_____________260_____________________________________________300\n_____________\|_______________________________________________\|\n5'-CUU...AAUUU_______U_____CCC______GG________________________-3'\n______________GAAGCCG_CGCCU___GCUGGU_____GAU_CUGGAAG____GUGAGU\n______________:\|\|\|\|\|:_\|:\|\|:___\|\|\|\|\|:_____:\|\|_\|\|\|\|\|\|\|____\|\|\|\|\|:\n______________UUUCGGU_GUGGG___CGACCG_____UUA_GACCUUC____CACUCG\n__________3'-U_______C_____C________AUUCA___U_______GUUA______UUACA...GCG-5'\n_____________\|________________________________________________\|\n_____________90_______________________________________________43\n	288 -- 294	54 -- 60	-44.5757 kcal/mol	13.1093 kcal/mol	14.9095 kcal/mol	260 300@LB@ \| \|@LB@5'-CUU...AAUUU U CCC GG -3'@LB@ GAAGCCG CGCCU GCUGGU GAU CUGGAAG GUGAGU@LB@ :\|\|\|\|\|: \|:\|\|: \|\|\|\|\|: :\|\| \|\|\|\|\|\|\| \|\|\|\|\|:@LB@ UUUCGGU GUGGG CGACCG UUA GACCUUC CACUCG@LB@ 3'-U C C AUUCA U GUUA UUACA...GCG-5'@LB@ \| \|@LB@ 90 43@LB@@LB@@LB@Energy -16.56 kcal/mol@LB@Hybridization Energy -44.5757 kcal/mol@LB@Unfolding Energy - mRNA 13.1093 kcal/mol@LB@Unfolding Energy - sRNA 14.9095 kcal/mol@LB@@LB@Position - mRNA 261 -- 300@LB@Position - sRNA 44 -- 89@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 54 -- 60@LB@
187	0.023	0.4113	b2311	ubiX	-11.39	0.112499	264 -- 277	17 -- 30	3-octaprenyl-4-hydroxybenzoate carboxy-lyase	_____________263____________278\n_____________\|______________\|\n5'-UGA...UAUUA________G_____UGUCA...AUC-3'\n______________CAGGUUCU_CGCGA\n______________\|\|\|\|\|\|\|\|_\|\|\|\|\|\n______________GUCCAAGA_GCGCU\n3'-UUU...CGAAA________G_____CCCAG...GCG-5'\n_____________\|______________\|\n_____________31_____________16\n	265 -- 271	23 -- 29	-23.8621 kcal/mol	5.17919 kcal/mol	7.29042 kcal/mol	263 278@LB@ \| \|@LB@5'-UGA...UAUUA G UGUCA...AUC-3'@LB@ CAGGUUCU CGCGA@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ GUCCAAGA GCGCU@LB@3'-UUU...CGAAA G CCCAG...GCG-5'@LB@ \| \|@LB@ 31 16@LB@@LB@@LB@Energy -11.39 kcal/mol@LB@Hybridization Energy -23.8621 kcal/mol@LB@Unfolding Energy - mRNA 5.17919 kcal/mol@LB@Unfolding Energy - sRNA 7.29042 kcal/mol@LB@@LB@Position - mRNA 264 -- 277@LB@Position - sRNA 17 -- 30@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 23 -- 29@LB@
130	0.01403	0.3627	b3531	bcsZ	-10.44	0.160598	268 -- 291	50 -- 82	endo-1 4-D-glucanase	_____________267_______________________________292\n_____________\|_________________________________\|\n5'-UCA...AGCCU_________CU______________________UUAAA...AGG-3'\n______________GUACCUGGC__GC_________CUGGGAGCAGU\n______________\|:\|\|\|:\|\|\|__\|\|_________\|\|\|\|:\|\|\|\|:\|\n______________CGUGGGCCG__CG_________GACCUUCGUUA\n___3'-UUUUCGGU_________AC__AUUCAUUAU___________CACUC...GCG-5'\n_____________\|_________________________________\|\n_____________83________________________________49\n	283 -- 289	52 -- 58	-33.5305 kcal/mol	8.70748 kcal/mol	14.3864 kcal/mol	267 292@LB@ \| \|@LB@5'-UCA...AGCCU CU UUAAA...AGG-3'@LB@ GUACCUGGC GC CUGGGAGCAGU@LB@ \|:\|\|\|:\|\|\| \|\| \|\|\|\|:\|\|\|\|:\|@LB@ CGUGGGCCG CG GACCUUCGUUA@LB@ 3'-UUUUCGGU AC AUUCAUUAU CACUC...GCG-5'@LB@ \| \|@LB@ 83 49@LB@@LB@@LB@Energy -10.44 kcal/mol@LB@Hybridization Energy -33.5305 kcal/mol@LB@Unfolding Energy - mRNA 8.70748 kcal/mol@LB@Unfolding Energy - sRNA 14.3864 kcal/mol@LB@@LB@Position - mRNA 268 -- 291@LB@Position - sRNA 50 -- 82@LB@Position Seed - mRNA 283 -- 289@LB@Position Seed - sRNA 52 -- 58@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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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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