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
79	0.007454	0.3134	b1912	pgsA	-16.66	0.014365	232 -- 294	1 -- 48	phosphatidylglycerophosphate synthetase	_____________231_____________________________________________________________295\n_____________\|_______________________________________________________________\|\n5'-GUC...UACAC__UU_C_____AUC___A__CCA________AUU______UUAUCUGCCUGUCA_________CGUUUG-3'\n______________UG__C_GUGUC___CUU_UC___UUCUUUGU___GGUCUU______________CCUGGUCGC\n______________\|\|__\|_:\|\|\|\|___\|\|\|_\|\|___\|\|\|\|::\|:___\|\|\|\|\|\|______________\|\|\|\|:\|\|\|\|\n______________AC__G_UACAG___GAA_AG___AAGAGGCG___CCAGAA______________GGACUAGCG\n3'-UUU...GUUAC__UC_U_____CAC______UCC________CUC_____________________________-5'\n_____________\|______________________________________________________________\|\n_____________49_____________________________________________________________1\n	288 -- 294	1 -- 7	-35.4585 kcal/mol	5.43289 kcal/mol	13.3693 kcal/mol	231 295@LB@ \| \|@LB@5'-GUC...UACAC UU C AUC A CCA AUU UUAUCUGCCUGUCA CGUUUG-3'@LB@ UG C GUGUC CUU UC UUCUUUGU GGUCUU CCUGGUCGC@LB@ \|\| \| :\|\|\|\| \|\|\| \|\| \|\|\|\|::\|: \|\|\|\|\|\| \|\|\|\|:\|\|\|\|@LB@ AC G UACAG GAA AG AAGAGGCG CCAGAA GGACUAGCG@LB@3'-UUU...GUUAC UC U CAC UCC CUC -5'@LB@ \| \|@LB@ 49 1@LB@@LB@@LB@Energy -16.66 kcal/mol@LB@Hybridization Energy -35.4585 kcal/mol@LB@Unfolding Energy - mRNA 5.43289 kcal/mol@LB@Unfolding Energy - sRNA 13.3693 kcal/mol@LB@@LB@Position - mRNA 232 -- 294@LB@Position - sRNA 1 -- 48@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 1 -- 7@LB@
154	0.01903	0.4072	b2823	ppdC	-17.47	0.010387	242 -- 260	40 -- 58	putative prepilin peptidase-dependent protein	_____________241_________________261\n_____________\|___________________\|\n5'-ACG...CUGCC___________U_______GUGUU...UCC-3'\n______________GGAGGUAAUGU_GGCGAUG\n______________\|\|\|:\|:\|\|\|\|\|_:\|\|:\|\|\|\n______________CCUUCGUUACA_UCGUUAC\n3'-UUU...UAUGA___________C_______AGCAC...GCG-5'\n_____________\|___________________\|\n_____________59__________________39\n	254 -- 260	40 -- 46	-26.2879 kcal/mol	5.60197 kcal/mol	3.21578 kcal/mol	241 261@LB@ \| \|@LB@5'-ACG...CUGCC U GUGUU...UCC-3'@LB@ GGAGGUAAUGU GGCGAUG@LB@ \|\|\|:\|:\|\|\|\|\| :\|\|:\|\|\|@LB@ CCUUCGUUACA UCGUUAC@LB@3'-UUU...UAUGA C AGCAC...GCG-5'@LB@ \| \|@LB@ 59 39@LB@@LB@@LB@Energy -17.47 kcal/mol@LB@Hybridization Energy -26.2879 kcal/mol@LB@Unfolding Energy - mRNA 5.60197 kcal/mol@LB@Unfolding Energy - sRNA 3.21578 kcal/mol@LB@@LB@Position - mRNA 242 -- 260@LB@Position - sRNA 40 -- 58@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 40 -- 46@LB@
152	0.0188	0.4072	b0950	pqiA	-8.64	0.302533	34 -- 75	1 -- 61	paraquat-inducible SoxRS-regulated inner membrane protein	_____________33_____________________________________________________________76\n_____________\|______________________________________________________________\|\n5'-CUG...UGAAC__________UCU__A______________________AAAAAAU_____GG__________AAAAU...GUC-3'\n______________GCUGGGAGUA___UG_AGC________________GUU_________GGU____CUGAUCGC\n______________:\|\|\|\|:\|\|:\|___\|\|_\|\|\|________________\|\|\|_________\|\|\|____\|\|\|\|\|\|\|\|\n______________UGACCUUCGU___AC_UCG________________CAA_________CCA____GACUAGCG\n3'-UUU...CAUUA__________UAC______UUACAGCACGAAAGUC___GAGGCGCUC___GAAG________-5'\n_____________\|_____________________________________________________________\|\n_____________62____________________________________________________________1\n	69 -- 75	1 -- 7	-32.0531 kcal/mol	9.29686 kcal/mol	14.1206 kcal/mol	33 76@LB@ \| \|@LB@5'-CUG...UGAAC UCU A AAAAAAU GG AAAAU...GUC-3'@LB@ GCUGGGAGUA UG AGC GUU GGU CUGAUCGC@LB@ :\|\|\|\|:\|\|:\| \|\| \|\|\| \|\|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ UGACCUUCGU AC UCG CAA CCA GACUAGCG@LB@3'-UUU...CAUUA UAC UUACAGCACGAAAGUC GAGGCGCUC GAAG -5'@LB@ \| \|@LB@ 62 1@LB@@LB@@LB@Energy -8.64 kcal/mol@LB@Hybridization Energy -32.0531 kcal/mol@LB@Unfolding Energy - mRNA 9.29686 kcal/mol@LB@Unfolding Energy - sRNA 14.1206 kcal/mol@LB@@LB@Position - mRNA 34 -- 75@LB@Position - sRNA 1 -- 61@LB@Position Seed - mRNA 69 -- 75@LB@Position Seed - sRNA 1 -- 7@LB@
84	0.008296	0.3318	b0892	rarA	-13.69	0.046473	183 -- 215	37 -- 66	recombination intermediate processing DNA-dependent ATPase	_____________182_________________________________216\n_____________\|___________________________________\|\n5'-CAA...UCAAC____GUA________CCUGA________UC_____CUCGA...AUU-3'\n______________GUAA_____GAGGCA_____GUGAGCAA__UGUCG\n______________\|\|\|\|_____\|\|:\|\|\|_____\|\|\|\|\|\|\|\|__\|\|\|\|\|\n______________CAUU_____CUUCGU_____CACUCGUU__ACAGC\n3'-UUU...CGAUU____AUGAC______UA__________________ACGAA...GCG-5'\n_____________\|___________________________________\|\n_____________67__________________________________36\n	202 -- 208	42 -- 48	-25.9915 kcal/mol	8.99953 kcal/mol	3.30551 kcal/mol	182 216@LB@ \| \|@LB@5'-CAA...UCAAC GUA CCUGA UC CUCGA...AUU-3'@LB@ GUAA GAGGCA GUGAGCAA UGUCG@LB@ \|\|\|\| \|\|:\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ CAUU CUUCGU CACUCGUU ACAGC@LB@3'-UUU...CGAUU AUGAC UA ACGAA...GCG-5'@LB@ \| \|@LB@ 67 36@LB@@LB@@LB@Energy -13.69 kcal/mol@LB@Hybridization Energy -25.9915 kcal/mol@LB@Unfolding Energy - mRNA 8.99953 kcal/mol@LB@Unfolding Energy - sRNA 3.30551 kcal/mol@LB@@LB@Position - mRNA 183 -- 215@LB@Position - sRNA 37 -- 66@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 42 -- 48@LB@
161	0.02011	0.4072	b2820	recB	-12.55	0.072418	202 -- 213	37 -- 48	exonuclease V (RecBCD complex) beta subunit	_____________201__________214\n_____________\|____________\|\n5'-GGC...AAGAA____________CCGAG...UUG-3'\n______________UGAGUGAUGUCG\n______________\|\|\|\|::\|\|\|\|\|\|\n______________ACUCGUUACAGC\n3'-UUU...GUUAC____________ACGAA...GCG-5'\n_____________\|____________\|\n_____________49___________36\n	207 -- 213	37 -- 43	-16.4196 kcal/mol	2.71715 kcal/mol	1.1567 kcal/mol	201 214@LB@ \| \|@LB@5'-GGC...AAGAA CCGAG...UUG-3'@LB@ UGAGUGAUGUCG@LB@ \|\|\|\|::\|\|\|\|\|\|@LB@ ACUCGUUACAGC@LB@3'-UUU...GUUAC ACGAA...GCG-5'@LB@ \| \|@LB@ 49 36@LB@@LB@@LB@Energy -12.55 kcal/mol@LB@Hybridization Energy -16.4196 kcal/mol@LB@Unfolding Energy - mRNA 2.71715 kcal/mol@LB@Unfolding Energy - sRNA 1.1567 kcal/mol@LB@@LB@Position - mRNA 202 -- 213@LB@Position - sRNA 37 -- 48@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 37 -- 43@LB@
15	0.001024	0.2294	b2822	recC	-16.38	0.016046	234 -- 264	37 -- 63	exonuclease V (RecBCD complex) gamma chain	_____________233______________________________265\n_____________\|________________________________\|\n5'-AGU...UGGAC___________GUU_________UUAU_____AACGC...AGA-3'\n______________GUGCUGGAAGC___GAUG_GAGU____UGUCG\n______________:\|:\|\|\|\|\|\|\|\|___:\|\|\|_\|\|\|:____\|\|\|\|\|\n______________UAUGACCUUCG___UUAC_CUCG____ACAGC\n3'-UUU...UUCAU__________________A____UU_______ACGAA...GCG-5'\n_____________\|________________________________\|\n_____________64_______________________________36\n	238 -- 244	53 -- 59	-30.8262 kcal/mol	11.1454 kcal/mol	3.30267 kcal/mol	233 265@LB@ \| \|@LB@5'-AGU...UGGAC GUU UUAU AACGC...AGA-3'@LB@ GUGCUGGAAGC GAUG GAGU UGUCG@LB@ :\|:\|\|\|\|\|\|\|\| :\|\|\| \|\|\|: \|\|\|\|\|@LB@ UAUGACCUUCG UUAC CUCG ACAGC@LB@3'-UUU...UUCAU A UU ACGAA...GCG-5'@LB@ \| \|@LB@ 64 36@LB@@LB@@LB@Energy -16.38 kcal/mol@LB@Hybridization Energy -30.8262 kcal/mol@LB@Unfolding Energy - mRNA 11.1454 kcal/mol@LB@Unfolding Energy - sRNA 3.30267 kcal/mol@LB@@LB@Position - mRNA 234 -- 264@LB@Position - sRNA 37 -- 63@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 53 -- 59@LB@
156	0.0192	0.4072	b0472	recR	-11.39	0.112512	68 -- 82	54 -- 68	gap repair protein	_____________67______________83\n_____________\|_______________\|\n5'-GUG...CGACA___A___________ACCUG...UUC-3'\n______________AAG_GAUGCUGGAAG\n______________\|\|\|_:\|\|:\|\|\|\|\|\|\|\n______________UUC_UUAUGACCUUC\n3'-UUU...ACCGA___A___________GUUAC...GCG-5'\n_____________\|_______________\|\n_____________69______________53\n	76 -- 82	54 -- 60	-16.6291 kcal/mol	2.52602 kcal/mol	2.71091 kcal/mol	67 83@LB@ \| \|@LB@5'-GUG...CGACA A ACCUG...UUC-3'@LB@ AAG GAUGCUGGAAG@LB@ \|\|\| :\|\|:\|\|\|\|\|\|\|@LB@ UUC UUAUGACCUUC@LB@3'-UUU...ACCGA A GUUAC...GCG-5'@LB@ \| \|@LB@ 69 53@LB@@LB@@LB@Energy -11.39 kcal/mol@LB@Hybridization Energy -16.6291 kcal/mol@LB@Unfolding Energy - mRNA 2.52602 kcal/mol@LB@Unfolding Energy - sRNA 2.71091 kcal/mol@LB@@LB@Position - mRNA 68 -- 82@LB@Position - sRNA 54 -- 68@LB@Position Seed - mRNA 76 -- 82@LB@Position Seed - sRNA 54 -- 60@LB@
95	0.009964	0.3393	b3902	rhaD	-16.21	0.017174	243 -- 283	43 -- 89	rhamnulose-1-phosphate aldolase	_____________242_______________________________________________284\n_____________\|_________________________________________________\|\n5'-AGA...UGAUC_______C____GA__C________AAG_____________________CAACG...UGA-3'\n______________AAAGCCA_CACC__CG_CUGGCUGA_____GCUGGGA______UGAGCG\n______________\|\|\|\|\|\|\|_\|\|\|\|__\|\|_\|\|\|\|\|\|:\|_____:\|\|\|\|:\|______\|\|\|\|\|:\n______________UUUCGGU_GUGG__GC_GACCGAUU_____UGACCUU______ACUCGU\n__________3'-U_______C________C________CAUUA_______CGUUAC______UACAG...GCG-5'\n_____________\|_________________________________________________\|\n_____________90________________________________________________42\n	271 -- 277	55 -- 61	-44.1539 kcal/mol	13.0365 kcal/mol	14.9102 kcal/mol	242 284@LB@ \| \|@LB@5'-AGA...UGAUC C GA C AAG CAACG...UGA-3'@LB@ AAAGCCA CACC CG CUGGCUGA GCUGGGA UGAGCG@LB@ \|\|\|\|\|\|\| \|\|\|\| \|\| \|\|\|\|\|\|:\| :\|\|\|\|:\| \|\|\|\|\|:@LB@ UUUCGGU GUGG GC GACCGAUU UGACCUU ACUCGU@LB@ 3'-U C C CAUUA CGUUAC UACAG...GCG-5'@LB@ \| \|@LB@ 90 42@LB@@LB@@LB@Energy -16.21 kcal/mol@LB@Hybridization Energy -44.1539 kcal/mol@LB@Unfolding Energy - mRNA 13.0365 kcal/mol@LB@Unfolding Energy - sRNA 14.9102 kcal/mol@LB@@LB@Position - mRNA 243 -- 283@LB@Position - sRNA 43 -- 89@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 55 -- 61@LB@
40	0.003423	0.2776	b3901	rhaM	-14.12	0.039141	284 -- 296	49 -- 61	L-rhamnose mutarotase	_____________283___________297\n_____________\|_____________\|\n5'-ACG...CCAGA_____________CUGA-3'\n______________ACUGGAAGCAGUG\n______________\|\|\|\|\|\|\|\|\|\|:\|\|\n______________UGACCUUCGUUAC\n3'-UUU...CAUUA_____________ACUCG...GCG-5'\n_____________\|_____________\|\n_____________62____________48\n	290 -- 296	49 -- 55	-21.3506 kcal/mol	4.21776 kcal/mol	3.00866 kcal/mol	283 297@LB@ \| \|@LB@5'-ACG...CCAGA CUGA-3'@LB@ ACUGGAAGCAGUG@LB@ \|\|\|\|\|\|\|\|\|\|:\|\|@LB@ UGACCUUCGUUAC@LB@3'-UUU...CAUUA ACUCG...GCG-5'@LB@ \| \|@LB@ 62 48@LB@@LB@@LB@Energy -14.12 kcal/mol@LB@Hybridization Energy -21.3506 kcal/mol@LB@Unfolding Energy - mRNA 4.21776 kcal/mol@LB@Unfolding Energy - sRNA 3.00866 kcal/mol@LB@@LB@Position - mRNA 284 -- 296@LB@Position - sRNA 49 -- 61@LB@Position Seed - mRNA 290 -- 296@LB@Position Seed - sRNA 49 -- 55@LB@
131	0.01424	0.3651	b0058	rluA	-14.42	0.034831	43 -- 63	40 -- 60	dual specificity 23S rRNA pseudouridine(746) tRNA pseudouridine(32) synthase SAM-dependent	_____________42____________________64\n_____________\|_____________________\|\n5'-CGU...CUCGU________UC__C_U______AACCC...UGU-3'\n______________CUGGAAGC__UG_G_GCAGUG\n______________\|\|\|\|\|\|\|\|__\|\|_\|_\|\|\|:\|\|\n______________GACCUUCG__AC_C_CGUUAC\n3'-UUU...AUUAU________UU__A_U______AGCAC...GCG-5'\n_____________\|_____________________\|\n_____________61____________________39\n	44 -- 50	53 -- 59	-25.1761 kcal/mol	7.45543 kcal/mol	3.29985 kcal/mol	42 64@LB@ \| \|@LB@5'-CGU...CUCGU UC C U AACCC...UGU-3'@LB@ CUGGAAGC UG G GCAGUG@LB@ \|\|\|\|\|\|\|\| \|\| \| \|\|\|:\|\|@LB@ GACCUUCG AC C CGUUAC@LB@3'-UUU...AUUAU UU A U AGCAC...GCG-5'@LB@ \| \|@LB@ 61 39@LB@@LB@@LB@Energy -14.42 kcal/mol@LB@Hybridization Energy -25.1761 kcal/mol@LB@Unfolding Energy - mRNA 7.45543 kcal/mol@LB@Unfolding Energy - sRNA 3.29985 kcal/mol@LB@@LB@Position - mRNA 43 -- 63@LB@Position - sRNA 40 -- 60@LB@Position Seed - mRNA 44 -- 50@LB@Position Seed - sRNA 53 -- 59@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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