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
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@
130	0.0142	0.3575	b0885	aat	-14.04	0.042507	189 -- 220	112 -- 144	leucyl/phenylalanyl-tRNA-protein transferase	_____________188_______________________________221\n_____________\|_________________________________\|\n5'-CGU...UUUUG________________CU_______________UCGCC...UUA-3'\n______________CGGUCAUGC_____GC__GGU___UCAGCUUUC\n______________\|:\|\|\|\|::\|_____\|\|__\|\|:___\|\|\|:\|\|\|\|\|\n______________GUCAGUGUG_____CG__CCG___AGUUGAAAG\n3'-UUU...UAUGA_________UACUA__U____UUC_________UCUUA...UAG-5'\n_____________\|_________________________________\|\n_____________145_______________________________111\n	214 -- 220	145 -- 151	-24.916 kcal/mol	8.31603 kcal/mol	8.21863 kcal/mol	188 221@LB@ \| \|@LB@5'-CGU...UUUUG CU UCGCC...UUA-3'@LB@ CGGUCAUGC GC GGU UCAGCUUUC@LB@ \|:\|\|\|\|::\| \|\| \|\|: \|\|\|:\|\|\|\|\|@LB@ GUCAGUGUG CG CCG AGUUGAAAG@LB@3'-UUU...UAUGA UACUA U UUC UCUUA...UAG-5'@LB@ \| \|@LB@ 145 111@LB@@LB@@LB@Energy -14.04 kcal/mol@LB@Hybridization Energy -24.916 kcal/mol@LB@Unfolding Energy - mRNA 8.31603 kcal/mol@LB@Unfolding Energy - sRNA 8.21863 kcal/mol@LB@@LB@Position - mRNA 189 -- 220@LB@Position - sRNA 112 -- 144@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 145 -- 151@LB@
110	0.01217	0.3575	b1324	tpx	-10.54	0.217228	251 -- 258	126 -- 133	lipid hydroperoxide peroxidase	_____________250____________259\n_____________\|______________\|\n5'-GCG...ACUCC______________GUCUG...AAG-3'\n______________UUGUUGUCGCGGUG\n______________\|:\|:\|\|\|\|\|\|\|\|\|:\n______________AGCGACAGCGCCAU\n3'-UUU...GUUGA______________UUUAU...UAG-5'\n_____________\|______________\|\n_____________134____________125\n	99 -- 105	48 -- 54	-22.761 kcal/mol	7.03952 kcal/mol	5.88061 kcal/mol	250 259@LB@ \| \|@LB@5'-GCG...ACUCC GUCUG...AAG-3'@LB@ UUGUUGUCGCGGUG@LB@ \|:\|:\|\|\|\|\|\|\|\|\|:@LB@ AGCGACAGCGCCAU@LB@3'-UUU...GUUGA UUUAU...UAG-5'@LB@ \| \|@LB@ 134 125@LB@@LB@@LB@Energy -10.54 kcal/mol@LB@Hybridization Energy -22.761 kcal/mol@LB@Unfolding Energy - mRNA 7.03952 kcal/mol@LB@Unfolding Energy - sRNA 5.88061 kcal/mol@LB@@LB@Position - mRNA 251 -- 258@LB@Position - sRNA 126 -- 133@LB@Position Seed - mRNA 99 -- 105@LB@Position Seed - sRNA 48 -- 54@LB@
196	0.0235	0.3833	b3105	yhaJ	-11.17	0.163135	292 -- 299	86 -- 93	LysR family putative transcriptional regulator	_____________291______300\n_____________\|________\|\n5'-CGG...UGAGC________G-3'\n______________UGGGACGC\n______________\|\|\|\|\|\|\|\|\n______________ACCCUGCG\n3'-UUU...GCAAC________AAUUG...UAG-5'\n_____________\|________\|\n_____________94_______85\n	293 -- 299	86 -- 92	-14.7688 kcal/mol	2.10679 kcal/mol	4.21973 kcal/mol	291 300@LB@ \| \|@LB@5'-CGG...UGAGC G-3'@LB@ UGGGACGC@LB@ \|\|\|\|\|\|\|\|@LB@ ACCCUGCG@LB@3'-UUU...GCAAC AAUUG...UAG-5'@LB@ \| \|@LB@ 94 85@LB@@LB@@LB@Energy -11.17 kcal/mol@LB@Hybridization Energy -14.7688 kcal/mol@LB@Unfolding Energy - mRNA 2.10679 kcal/mol@LB@Unfolding Energy - sRNA 4.21973 kcal/mol@LB@@LB@Position - mRNA 292 -- 299@LB@Position - sRNA 86 -- 93@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 86 -- 92@LB@
149	0.01599	0.3612	b3236	mdh	-10.77	0.195799	223 -- 232	196 -- 205	malate dehydrogenase NAD(P)-binding	_____________222_____233\n_____________\|_______\|\n5'-GUU...AUGAA_______GUCCU...AUG-3'\n______________AGUCGCA\n______________\|\|\|\|:\|\|\n______________UCAGUGU\n3'-UUU...AUGAG_______GUACU...UAG-5'\n_____________\|_______\|\n_____________206_____195\n	206 -- 212	169 -- 175	-8.87418 kcal/mol	1.40028 kcal/mol	0.26566 kcal/mol	222 233@LB@ \| \|@LB@5'-GUU...AUGAA GUCCU...AUG-3'@LB@ AGUCGCA@LB@ \|\|\|\|:\|\|@LB@ UCAGUGU@LB@3'-UUU...AUGAG GUACU...UAG-5'@LB@ \| \|@LB@ 206 195@LB@@LB@@LB@Energy -10.77 kcal/mol@LB@Hybridization Energy -8.87418 kcal/mol@LB@Unfolding Energy - mRNA 1.40028 kcal/mol@LB@Unfolding Energy - sRNA 0.26566 kcal/mol@LB@@LB@Position - mRNA 223 -- 232@LB@Position - sRNA 196 -- 205@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 169 -- 175@LB@
52	0.005023	0.3217	b0403	malZ	-9.64	0.320537	253 -- 286	155 -- 185	maltodextrin glucosidase	_____________252___________________________287\n_____________\|_____________________________\|\n5'-UUU...UCAAC_____________U____C__A_______AGACC...AGC-3'\n______________UGCUCA_UUACAC_GUGG_UG_CGGGCGA\n______________\|:\|\|\|\|_\|:\|\|\|\|_:\|\|:_\|\|_\|:\|\|\|:\|\n______________AUGAGU_AGUGUG_UACU_AC_GUCCGUU\n3'-UUU...UGGUU______C______________________CAGUU...UAG-5'\n_____________\|_____________________________\|\n_____________186___________________________154\n	280 -- 286	155 -- 161	-27.4446 kcal/mol	6.9929 kcal/mol	7.82707 kcal/mol	252 287@LB@ \| \|@LB@5'-UUU...UCAAC U C A AGACC...AGC-3'@LB@ UGCUCA UUACAC GUGG UG CGGGCGA@LB@ \|:\|\|\|\| \|:\|\|\|\| :\|\|: \|\| \|:\|\|\|:\|@LB@ AUGAGU AGUGUG UACU AC GUCCGUU@LB@3'-UUU...UGGUU C CAGUU...UAG-5'@LB@ \| \|@LB@ 186 154@LB@@LB@@LB@Energy -9.64 kcal/mol@LB@Hybridization Energy -27.4446 kcal/mol@LB@Unfolding Energy - mRNA 6.9929 kcal/mol@LB@Unfolding Energy - sRNA 7.82707 kcal/mol@LB@@LB@Position - mRNA 253 -- 286@LB@Position - sRNA 155 -- 185@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 155 -- 161@LB@
17	0.001014	0.2007	b4032	malG	-14.09	0.041561	127 -- 139	193 -- 205	maltose transporter subunit	_____________126___________140\n_____________\|_____________\|\n5'-CGU...UCUUC_____________CGCUG...UGG-3'\n______________CUGCUGGUGGGUG\n______________\|\|\|\|\|\|\|:\|\|\|\|\|\n______________GACGACCGCCCAC\n3'-UUU...UAUUA_____________UAAAA...UAG-5'\n_____________\|_____________\|\n_____________206___________192\n	132 -- 138	194 -- 200	-26.9183 kcal/mol	7.69341 kcal/mol	9.06058 kcal/mol	126 140@LB@ \| \|@LB@5'-CGU...UCUUC CGCUG...UGG-3'@LB@ CUGCUGGUGGGUG@LB@ \|\|\|\|\|\|\|:\|\|\|\|\|@LB@ GACGACCGCCCAC@LB@3'-UUU...UAUUA UAAAA...UAG-5'@LB@ \| \|@LB@ 206 192@LB@@LB@@LB@Energy -14.09 kcal/mol@LB@Hybridization Energy -26.9183 kcal/mol@LB@Unfolding Energy - mRNA 7.69341 kcal/mol@LB@Unfolding Energy - sRNA 9.06058 kcal/mol@LB@@LB@Position - mRNA 127 -- 139@LB@Position - sRNA 193 -- 205@LB@Position Seed - mRNA 132 -- 138@LB@Position Seed - sRNA 194 -- 200@LB@
189	0.02188	0.3833	b4033	malF	-11.66	0.130598	273 -- 284	194 -- 205	maltose transporter subunit	_____________272__________285\n_____________\|____________\|\n5'-CUG...UCGGC____________UACCU...UAA-3'\n______________CUGCUGGUGGGU\n______________\|\|\|\|\|\|\|:\|\|\|\|\n______________GACGACCGCCCA\n3'-UUU...UAUUA____________CUAAA...UAG-5'\n_____________\|____________\|\n_____________206__________193\n	278 -- 284	194 -- 200	-24.1506 kcal/mol	7.59361 kcal/mol	9.05892 kcal/mol	272 285@LB@ \| \|@LB@5'-CUG...UCGGC UACCU...UAA-3'@LB@ CUGCUGGUGGGU@LB@ \|\|\|\|\|\|\|:\|\|\|\|@LB@ GACGACCGCCCA@LB@3'-UUU...UAUUA CUAAA...UAG-5'@LB@ \| \|@LB@ 206 193@LB@@LB@@LB@Energy -11.66 kcal/mol@LB@Hybridization Energy -24.1506 kcal/mol@LB@Unfolding Energy - mRNA 7.59361 kcal/mol@LB@Unfolding Energy - sRNA 9.05892 kcal/mol@LB@@LB@Position - mRNA 273 -- 284@LB@Position - sRNA 194 -- 205@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 194 -- 200@LB@
165	0.01884	0.3812	b3291	mscL	-11.12	0.167422	252 -- 267	193 -- 208	mechanosensitive channel protein high conductance	_____________251_____268\n_____________\|_______\|\n5'-UGU...UGUCG_______AGGGA...UCU-3'\n______________GCUUCAU\n______________\|\|\|\|\|\|\|\n______________CGAAGUA\n3'-UUU...GGGAA_______G-5'\n_____________\|_______\|\n_____________209_____192\n	182 -- 188	2 -- 8	-9.41561 kcal/mol	2.23742 kcal/mol	0.70263 kcal/mol	251 268@LB@ \| \|@LB@5'-UGU...UGUCG AGGGA...UCU-3'@LB@ GCUUCAU@LB@ \|\|\|\|\|\|\|@LB@ CGAAGUA@LB@3'-UUU...GGGAA G-5'@LB@ \| \|@LB@ 209 192@LB@@LB@@LB@Energy -11.12 kcal/mol@LB@Hybridization Energy -9.41561 kcal/mol@LB@Unfolding Energy - mRNA 2.23742 kcal/mol@LB@Unfolding Energy - sRNA 0.70263 kcal/mol@LB@@LB@Position - mRNA 252 -- 267@LB@Position - sRNA 193 -- 208@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 2 -- 8@LB@
169	0.01937	0.3812	b4557	yidD	-14.07	0.041992	2 -- 13	11 -- 22	membrane protein insertion efficiency factor UPF0161 family inner membrane protein	_____________1______________________14\n_____________\|______________________\|\n__________5'-C____________GUAUCG____UUACA...UCA-3'\n______________UGGGGCAUCCCC_______GUC\n______________\|\|\|\|\|\|\|:\|\|\|\|_______:\|\|\n______________ACCCCGUGGGGG_______UAG\n3'-UUU...UGCGU____________AACGAAG___-5'\n_____________\|_____________________\|\n_____________23____________________11\n	7 -- 13	11 -- 17	-28.608 kcal/mol	8.24927 kcal/mol	10.7363 kcal/mol	1 14@LB@ \| \|@LB@ 5'-C GUAUCG UUACA...UCA-3'@LB@ UGGGGCAUCCCC GUC@LB@ \|\|\|\|\|\|\|:\|\|\|\| :\|\|@LB@ ACCCCGUGGGGG UAG@LB@3'-UUU...UGCGU AACGAAG -5'@LB@ \| \|@LB@ 23 11@LB@@LB@@LB@Energy -14.07 kcal/mol@LB@Hybridization Energy -28.608 kcal/mol@LB@Unfolding Energy - mRNA 8.24927 kcal/mol@LB@Unfolding Energy - sRNA 10.7363 kcal/mol@LB@@LB@Position - mRNA 2 -- 13@LB@Position - sRNA 11 -- 22@LB@Position Seed - mRNA 7 -- 13@LB@Position Seed - sRNA 11 -- 17@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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