Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
131	0.01426	0.3575	b0048	folA	-12.08	0.107221	135 -- 211	115 -- 187	dihydrofolate reductase	_____________134_________212\n_____________\|___________\|\n5'-UCA...UUGUU___________GUAAU...GCA-3'\n______________UUUGUUUCAUU\n______________:\|\|\|:\|\|\|\|\|:\n______________GAACGAAGUAG\n3'-UUU...UGGGG___________-5'\n_____________\|__________\|\n_____________188________115\n	56 -- 62	1 -- 7	-10.5455 kcal/mol	1.7602 kcal/mol	1.03329 kcal/mol	134 212@LB@ \| \|@LB@5'-UCA...UUGUU GUAAU...GCA-3'@LB@ UUUGUUUCAUU@LB@ :\|\|\|:\|\|\|\|\|:@LB@ GAACGAAGUAG@LB@3'-UUU...UGGGG -5'@LB@ \| \|@LB@ 188 115@LB@@LB@@LB@Energy -12.08 kcal/mol@LB@Hybridization Energy -10.5455 kcal/mol@LB@Unfolding Energy - mRNA 1.7602 kcal/mol@LB@Unfolding Energy - sRNA 1.03329 kcal/mol@LB@@LB@Position - mRNA 135 -- 211@LB@Position - sRNA 115 -- 187@LB@Position Seed - mRNA 56 -- 62@LB@Position Seed - sRNA 1 -- 7@LB@
132	0.0143	0.3575	b0147	ligT	-9.89	0.288456	69 -- 117	16 -- 69	2'-5' RNA ligase	_____________68__________________________________118\n_____________\|___________________________________\|\n5'-CCA...AAGUA______GUA_G___GCAGCAA_______C_A____ACAAA...CGG-3'\n______________AUUCAG___A_ACG_______CGGGCAA_G_CGAC\n______________\|:\|\|\|\|___\|_\|\|:_______\|:\|\|\|\|\|_\|_\|:\|\|\n______________UGAGUC___U_UGU_______GUCCGUU_C_GUUG\n3'-UUU...GGUUA______AG__G___ACUAC___________A____AAAGU...UAG-5'\n_____________\|___________________________________\|\n_____________70__________________________________15\n	112 -- 118	155 -- 161	-21.4956 kcal/mol	4.52534 kcal/mol	8.18567 kcal/mol	68 118@LB@ \| \|@LB@5'-CCA...AAGUA GUA G GCAGCAA C A ACAAA...CGG-3'@LB@ AUUCAG A ACG CGGGCAA G CGAC@LB@ \|:\|\|\|\| \| \|\|: \|:\|\|\|\|\| \| \|:\|\|@LB@ UGAGUC U UGU GUCCGUU C GUUG@LB@3'-UUU...GGUUA AG G ACUAC A AAAGU...UAG-5'@LB@ \| \|@LB@ 70 15@LB@@LB@@LB@Energy -9.89 kcal/mol@LB@Hybridization Energy -21.4956 kcal/mol@LB@Unfolding Energy - mRNA 4.52534 kcal/mol@LB@Unfolding Energy - sRNA 8.18567 kcal/mol@LB@@LB@Position - mRNA 69 -- 117@LB@Position - sRNA 16 -- 69@LB@Position Seed - mRNA 112 -- 118@LB@Position Seed - sRNA 155 -- 161@LB@
133	0.01432	0.3575	b2342	fadI	-11.00	0.176527	78 -- 109	125 -- 153	beta-ketoacyl-CoA thiolase anaerobic subunit	_____________77________________________________110\n_____________\|_________________________________\|\n5'-UCC...UCUCU__UU_____CUCUC________UAGC_______UUCCC...AUG-3'\n______________UC__CUUUU_____UGU_GUCA____UCCCACU\n______________\|\|__\|\|\|\|:_____\|\|:_\|\|\|\|____\|\|\|\|\|\|\|\n______________AG__GAAAG_____ACG_CAGU____AGGGUGA\n3'-UUU...CGUUC__UU_____UCUUA___C_______________CGUAG...UAG-5'\n_____________\|_________________________________\|\n_____________154_______________________________124\n	103 -- 109	125 -- 131	-19.0317 kcal/mol	1.6674 kcal/mol	9.91012 kcal/mol	77 110@LB@ \| \|@LB@5'-UCC...UCUCU UU CUCUC UAGC UUCCC...AUG-3'@LB@ UC CUUUU UGU GUCA UCCCACU@LB@ \|\| \|\|\|\|: \|\|: \|\|\|\| \|\|\|\|\|\|\|@LB@ AG GAAAG ACG CAGU AGGGUGA@LB@3'-UUU...CGUUC UU UCUUA C CGUAG...UAG-5'@LB@ \| \|@LB@ 154 124@LB@@LB@@LB@Energy -11.00 kcal/mol@LB@Hybridization Energy -19.0317 kcal/mol@LB@Unfolding Energy - mRNA 1.6674 kcal/mol@LB@Unfolding Energy - sRNA 9.91012 kcal/mol@LB@@LB@Position - mRNA 78 -- 109@LB@Position - sRNA 125 -- 153@LB@Position Seed - mRNA 103 -- 109@LB@Position Seed - sRNA 125 -- 131@LB@
134	0.01437	0.3575	b1798	leuE	-11.20	0.161096	19 -- 44	168 -- 191	leucine efflux protein	_____________18_________________________45\n_____________\|__________________________\|\n5'-UGC...AGAAU________________UGCCGA____UACCC...AAA-3'\n______________UUUUACGCCAGUAUUU______GCAC\n______________\|\|\|\|\|\|:\|\|\|:\|\|:\|:______:\|\|\|\n______________AAAAUGUGGUUAUGAG______UGUG\n3'-UUU...CCACU________________UCAG______UACUA...UAG-5'\n_____________\|__________________________\|\n_____________192________________________167\n	26 -- 32	178 -- 184	-22.4094 kcal/mol	4.02149 kcal/mol	4.92826 kcal/mol	18 45@LB@ \| \|@LB@5'-UGC...AGAAU UGCCGA UACCC...AAA-3'@LB@ UUUUACGCCAGUAUUU GCAC@LB@ \|\|\|\|\|\|:\|\|\|:\|\|:\|: :\|\|\|@LB@ AAAAUGUGGUUAUGAG UGUG@LB@3'-UUU...CCACU UCAG UACUA...UAG-5'@LB@ \| \|@LB@ 192 167@LB@@LB@@LB@Energy -11.20 kcal/mol@LB@Hybridization Energy -22.4094 kcal/mol@LB@Unfolding Energy - mRNA 4.02149 kcal/mol@LB@Unfolding Energy - sRNA 4.92826 kcal/mol@LB@@LB@Position - mRNA 19 -- 44@LB@Position - sRNA 168 -- 191@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 178 -- 184@LB@
135	0.01453	0.3575	b2934	cmtB	-15.85	0.018111	229 -- 275	145 -- 186	putative mannitol-specific enzyme IIA component of PTS	_____________228___________________276\n_____________\|_____________________\|\n5'-AUA...AGAAU_____________________UCAGC...UGG-3'\n______________CAUCAAU_CUCAGUUAUACAU\n______________\|\|:\|\|\|\|_\|\|\|\|\|\|:\|:\|\|\|\|\n______________GUGGUUA_GAGUCAGUGUGUA\n3'-UUU...AAAAU_______U_____________CUACG...UAG-5'\n_____________\|_____________________\|\n_____________187___________________144\n	242 -- 248	166 -- 172	-24.8158 kcal/mol	1.5387 kcal/mol	5.06797 kcal/mol	228 276@LB@ \| \|@LB@5'-AUA...AGAAU UCAGC...UGG-3'@LB@ CAUCAAU CUCAGUUAUACAU@LB@ \|\|:\|\|\|\| \|\|\|\|\|\|:\|:\|\|\|\|@LB@ GUGGUUA GAGUCAGUGUGUA@LB@3'-UUU...AAAAU U CUACG...UAG-5'@LB@ \| \|@LB@ 187 144@LB@@LB@@LB@Energy -15.85 kcal/mol@LB@Hybridization Energy -24.8158 kcal/mol@LB@Unfolding Energy - mRNA 1.5387 kcal/mol@LB@Unfolding Energy - sRNA 5.06797 kcal/mol@LB@@LB@Position - mRNA 229 -- 275@LB@Position - sRNA 145 -- 186@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 166 -- 172@LB@
136	0.01456	0.3575	b0369	hemB	-9.31	0.367566	203 -- 221	75 -- 90	5-aminolevulinate dehydratase (porphobilinogen synthase)	_____________202________________222\n_____________\|__________________\|\n5'-CCA...UAAAA_______ACCC_______GGUAU...UGC-3'\n______________CAUCCCU____UGCUUCA\n______________\|\|:\|\|\|:____\|\|\|\|\|\|\|\n______________GUGGGGG____ACGAAGU\n3'-UUU...ACCCC_______A__________AG-5'\n_____________\|__________________\|\n_____________91_________________74\n	153 -- 159	3 -- 9	-17.8942 kcal/mol	1.92924 kcal/mol	7.09151 kcal/mol	202 222@LB@ \| \|@LB@5'-CCA...UAAAA ACCC GGUAU...UGC-3'@LB@ CAUCCCU UGCUUCA@LB@ \|\|:\|\|\|: \|\|\|\|\|\|\|@LB@ GUGGGGG ACGAAGU@LB@3'-UUU...ACCCC A AG-5'@LB@ \| \|@LB@ 91 74@LB@@LB@@LB@Energy -9.31 kcal/mol@LB@Hybridization Energy -17.8942 kcal/mol@LB@Unfolding Energy - mRNA 1.92924 kcal/mol@LB@Unfolding Energy - sRNA 7.09151 kcal/mol@LB@@LB@Position - mRNA 203 -- 221@LB@Position - sRNA 75 -- 90@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 3 -- 9@LB@
137	0.01486	0.3575	b3967	murI	-16.98	0.010727	107 -- 167	42 -- 96	glutamate racemase	_____________106__________________________168\n_____________\|____________________________\|\n5'-GUU...GACUG________ACU_____________G___UCGCU...GGU-3'\n______________GGGU_AUU___UAUCAGUAUUUAG_CAC\n______________\|\|\|\|_\|\|\|___:\|:\|\|:\|\|:\|:\|\|_\|\|\|\n______________CCCA_UAA___GUGGUUAUGAGUC_GUG\n3'-UUU...GACCG____C___AAU_____________A___UGUAC...UAG-5'\n_____________\|____________________________\|\n_____________97___________________________41\n	35 -- 41	174 -- 180	-22.1424 kcal/mol	5.45848 kcal/mol	5.03792 kcal/mol	106 168@LB@ \| \|@LB@5'-GUU...GACUG ACU G UCGCU...GGU-3'@LB@ GGGU AUU UAUCAGUAUUUAG CAC@LB@ \|\|\|\| \|\|\| :\|:\|\|:\|\|:\|:\|\| \|\|\|@LB@ CCCA UAA GUGGUUAUGAGUC GUG@LB@3'-UUU...GACCG C AAU A UGUAC...UAG-5'@LB@ \| \|@LB@ 97 41@LB@@LB@@LB@Energy -16.98 kcal/mol@LB@Hybridization Energy -22.1424 kcal/mol@LB@Unfolding Energy - mRNA 5.45848 kcal/mol@LB@Unfolding Energy - sRNA 5.03792 kcal/mol@LB@@LB@Position - mRNA 107 -- 167@LB@Position - sRNA 42 -- 96@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 174 -- 180@LB@
138	0.01487	0.3575	b3771	ilvD	-15.83	0.018324	35 -- 66	67 -- 98	dihydroxyacid dehydratase	_____________34______67\n_____________\|_______\|\n5'-GCG...AAAAA_______GCACG...GUA-3'\n______________UGGGACG\n______________\|\|\|\|\|\|\|\n______________ACCCUGC\n3'-UUU...GCAAC_______GAAUU...UAG-5'\n_____________\|_______\|\n_____________99______66\n	147 -- 153	87 -- 93	-12.7493 kcal/mol	2.26202 kcal/mol	4.21173 kcal/mol	34 67@LB@ \| \|@LB@5'-GCG...AAAAA GCACG...GUA-3'@LB@ UGGGACG@LB@ \|\|\|\|\|\|\|@LB@ ACCCUGC@LB@3'-UUU...GCAAC GAAUU...UAG-5'@LB@ \| \|@LB@ 99 66@LB@@LB@@LB@Energy -15.83 kcal/mol@LB@Hybridization Energy -12.7493 kcal/mol@LB@Unfolding Energy - mRNA 2.26202 kcal/mol@LB@Unfolding Energy - sRNA 4.21173 kcal/mol@LB@@LB@Position - mRNA 35 -- 66@LB@Position - sRNA 67 -- 98@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 87 -- 93@LB@
139	0.01488	0.3575	b2167	fruA	-12.05	0.108648	223 -- 242	167 -- 187	fused fructose-specific PTS enzymes: IIBcomponent/IIC components	_____________222___________________243\n_____________\|_____________________\|\n5'-CGC...UAUUG_________________G___CGCGC...AAA-3'\n______________ACGCUAAU_CUCGGUCA_GCA\n______________\|\|:\|:\|\|\|_\|\|\|:\|\|\|\|_:\|\|\n______________UGUGGUUA_GAGUCAGU_UGU\n3'-UUU...UAAAA________U________G___ACUAC...UAG-5'\n_____________\|_____________________\|\n_____________188___________________166\n	232 -- 238	171 -- 177	-25.758 kcal/mol	6.7352 kcal/mol	5.05492 kcal/mol	222 243@LB@ \| \|@LB@5'-CGC...UAUUG G CGCGC...AAA-3'@LB@ ACGCUAAU CUCGGUCA GCA@LB@ \|\|:\|:\|\|\| \|\|\|:\|\|\|\| :\|\|@LB@ UGUGGUUA GAGUCAGU UGU@LB@3'-UUU...UAAAA U G ACUAC...UAG-5'@LB@ \| \|@LB@ 188 166@LB@@LB@@LB@Energy -12.05 kcal/mol@LB@Hybridization Energy -25.758 kcal/mol@LB@Unfolding Energy - mRNA 6.7352 kcal/mol@LB@Unfolding Energy - sRNA 5.05492 kcal/mol@LB@@LB@Position - mRNA 223 -- 242@LB@Position - sRNA 167 -- 187@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 171 -- 177@LB@
140	0.01495	0.3575	b2415	ptsH	-9.89	0.288161	112 -- 122	24 -- 34	phosphohistidinoprotein-hexose phosphotransferase component of PTS system (Hpr)	_____________111____________123\n_____________\|______________\|\n5'-UUG...CAAUA_____UA_______ACCGC...UUA-3'\n______________CAGGC__AAGUCGA\n______________\|\|\|\|\|__\|\|\|\|\|:\|\n______________GUCCG__UUCAGUU\n3'-UUU...ACUAC______________GAAAG...UAG-5'\n_____________\|______________\|\n_____________35_____________23\n	138 -- 144	150 -- 156	-14.4294 kcal/mol	3.35524 kcal/mol	6.54796 kcal/mol	111 123@LB@ \| \|@LB@5'-UUG...CAAUA UA ACCGC...UUA-3'@LB@ CAGGC AAGUCGA@LB@ \|\|\|\|\| \|\|\|\|\|:\|@LB@ GUCCG UUCAGUU@LB@3'-UUU...ACUAC GAAAG...UAG-5'@LB@ \| \|@LB@ 35 23@LB@@LB@@LB@Energy -9.89 kcal/mol@LB@Hybridization Energy -14.4294 kcal/mol@LB@Unfolding Energy - mRNA 3.35524 kcal/mol@LB@Unfolding Energy - sRNA 6.54796 kcal/mol@LB@@LB@Position - mRNA 112 -- 122@LB@Position - sRNA 24 -- 34@LB@Position Seed - mRNA 138 -- 144@LB@Position Seed - sRNA 150 -- 156@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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