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
161	0.01797	0.3749	b1921	fliZ	-13.03	0.068461	73 -- 137	125 -- 204	RpoS antagonist; putative regulator of FliA activity	_____________72__________________________________________138\n_____________\|___________________________________________\|\n5'-UGC...GAGGU_______AU______G___C_G___________GC________UAUUA...AUC-3'\n______________CGGG_GA_____CGC_GGU_A_UCAGUUACACA_____CAGGC\n______________\|\|\|\|_\|\|_____\|:\|_::\|_\|_\|\|\|\|\|:\|\|\|\|\|_____\|\|\|\|\|\n______________GCCC_CU_____GUG_UUA_U_AGUCAGUGUGU_____GUCCG\n3'-UUU...CGACC____A__AAAAU___G_____G___________ACUAC_____UUCAG...UAG-5'\n_____________\|___________________________________________\|\n_____________205_________________________________________124\n	105 -- 111	167 -- 173	-36.0631 kcal/mol	8.93512 kcal/mol	13.9606 kcal/mol	72 138@LB@ \| \|@LB@5'-UGC...GAGGU AU G C G GC UAUUA...AUC-3'@LB@ CGGG GA CGC GGU A UCAGUUACACA CAGGC@LB@ \|\|\|\| \|\| \|:\| ::\| \| \|\|\|\|\|:\|\|\|\|\| \|\|\|\|\|@LB@ GCCC CU GUG UUA U AGUCAGUGUGU GUCCG@LB@3'-UUU...CGACC A AAAAU G G ACUAC UUCAG...UAG-5'@LB@ \| \|@LB@ 205 124@LB@@LB@@LB@Energy -13.03 kcal/mol@LB@Hybridization Energy -36.0631 kcal/mol@LB@Unfolding Energy - mRNA 8.93512 kcal/mol@LB@Unfolding Energy - sRNA 13.9606 kcal/mol@LB@@LB@Position - mRNA 73 -- 137@LB@Position - sRNA 125 -- 204@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 167 -- 173@LB@
162	0.01805	0.3749	b2499	purM	-13.07	0.067336	182 -- 195	13 -- 27	phosphoribosylaminoimidazole synthetase	_____________181______196\n_____________\|________\|\n__________5'-U________AUGGU...CGC-3'\n______________AUAUUCAG\n______________\|\|\|:\|\|\|\|\n______________UAUGAGUC\n3'-UUU...GUGGU________AGUGU...UAG-5'\n_____________\|________\|\n_____________28_______12\n	3 -- 9	174 -- 180	-7.89877 kcal/mol	1.882 kcal/mol	0.273058 kcal/mol	181 196@LB@ \| \|@LB@ 5'-U AUGGU...CGC-3'@LB@ AUAUUCAG@LB@ \|\|\|:\|\|\|\|@LB@ UAUGAGUC@LB@3'-UUU...GUGGU AGUGU...UAG-5'@LB@ \| \|@LB@ 28 12@LB@@LB@@LB@Energy -13.07 kcal/mol@LB@Hybridization Energy -7.89877 kcal/mol@LB@Unfolding Energy - mRNA 1.882 kcal/mol@LB@Unfolding Energy - sRNA 0.273058 kcal/mol@LB@@LB@Position - mRNA 182 -- 195@LB@Position - sRNA 13 -- 27@LB@Position Seed - mRNA 3 -- 9@LB@Position Seed - sRNA 174 -- 180@LB@
163	0.01822	0.376	b1073	flgB	-9.73	0.308533	172 -- 220	24 -- 70	flagellar component of cell-proximal portion of basal-body rod	_____________171_______221\n_____________\|_________\|\n5'-UGA...AACAU_________CG-3'\n______________CGCCAAUGC\n______________\|:\|\|\|\|\|:\|\n______________GUGGUUAUG\n3'-UUU...AAAAU_________AGUCA...UAG-5'\n_____________\|_________\|\n_____________71________23\n	292 -- 298	178 -- 184	-11.5881 kcal/mol	1.63005 kcal/mol	3.31726 kcal/mol	171 221@LB@ \| \|@LB@5'-UGA...AACAU CG-3'@LB@ CGCCAAUGC@LB@ \|:\|\|\|\|\|:\|@LB@ GUGGUUAUG@LB@3'-UUU...AAAAU AGUCA...UAG-5'@LB@ \| \|@LB@ 71 23@LB@@LB@@LB@Energy -9.73 kcal/mol@LB@Hybridization Energy -11.5881 kcal/mol@LB@Unfolding Energy - mRNA 1.63005 kcal/mol@LB@Unfolding Energy - sRNA 3.31726 kcal/mol@LB@@LB@Position - mRNA 172 -- 220@LB@Position - sRNA 24 -- 70@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 178 -- 184@LB@
164	0.01856	0.3808	b0715	abrB	-11.36	0.150074	79 -- 113	125 -- 160	regulator of aidB expression; inner membrane protein	_____________78_____________114\n_____________\|______________\|\n5'-GGC...CGGCG______U_______GCCGA-3'\n______________GCGCUA_UACUUGG\n______________:\|:\|:\|_\|\|\|\|::\|\n______________UGUGGU_AUGAGUC\n3'-UUU...UAAAA______U_______AGUGU...UAG-5'\n_____________\|______________\|\n_____________161____________124\n	289 -- 295	174 -- 180	-13.5584 kcal/mol	1.79119 kcal/mol	3.6661 kcal/mol	78 114@LB@ \| \|@LB@5'-GGC...CGGCG U GCCGA-3'@LB@ GCGCUA UACUUGG@LB@ :\|:\|:\| \|\|\|\|::\|@LB@ UGUGGU AUGAGUC@LB@3'-UUU...UAAAA U AGUGU...UAG-5'@LB@ \| \|@LB@ 161 124@LB@@LB@@LB@Energy -11.36 kcal/mol@LB@Hybridization Energy -13.5584 kcal/mol@LB@Unfolding Energy - mRNA 1.79119 kcal/mol@LB@Unfolding Energy - sRNA 3.6661 kcal/mol@LB@@LB@Position - mRNA 79 -- 113@LB@Position - sRNA 125 -- 160@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 174 -- 180@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@
166	0.01886	0.3812	b3300	secY	-11.48	0.141920	168 -- 177	196 -- 205	preprotein translocase membrane subunit	_____________167_______________178\n_____________\|_________________\|\n5'-CCU...UCGAA____C_G__________CGAGG...UCC-3'\n______________GCUG_U_GCGGUAAAAU\n______________\|\|\|\|_\|_\|\|\|\|\|\|\|\|\|\|\n______________CGAC_A_CGCCAUUUUA\n3'-UUU...UGAAG______G__________UCACG...UAG-5'\n_____________\|_________________\|\n_____________206_______________195\n	177 -- 183	44 -- 50	-20.9884 kcal/mol	6.84834 kcal/mol	6.15722 kcal/mol	167 178@LB@ \| \|@LB@5'-CCU...UCGAA C G CGAGG...UCC-3'@LB@ GCUG U GCGGUAAAAU@LB@ \|\|\|\| \| \|\|\|\|\|\|\|\|\|\|@LB@ CGAC A CGCCAUUUUA@LB@3'-UUU...UGAAG G UCACG...UAG-5'@LB@ \| \|@LB@ 206 195@LB@@LB@@LB@Energy -11.48 kcal/mol@LB@Hybridization Energy -20.9884 kcal/mol@LB@Unfolding Energy - mRNA 6.84834 kcal/mol@LB@Unfolding Energy - sRNA 6.15722 kcal/mol@LB@@LB@Position - mRNA 168 -- 177@LB@Position - sRNA 196 -- 205@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 44 -- 50@LB@
167	0.01932	0.3812	b2912	fau	-13.57	0.053124	153 -- 189	109 -- 152	5-formyltetrahydrofolate cyclo-ligase family protein	_____________152__________190\n_____________\|____________\|\n5'-GAA...UGAGC____________GUCCG...UGG-3'\n______________AUGCUCGGUC_C\n______________\|\|:\|\|\|:\|\|\|_\|\n______________UAUGAGUCAG_G\n3'-UUU...GUGGU__________U_UGUAC...UAG-5'\n_____________\|____________\|\n_____________153__________108\n	31 -- 37	172 -- 178	-13.9133 kcal/mol	3.57919 kcal/mol	0.28482 kcal/mol	152 190@LB@ \| \|@LB@5'-GAA...UGAGC GUCCG...UGG-3'@LB@ AUGCUCGGUC C@LB@ \|\|:\|\|\|:\|\|\| \|@LB@ UAUGAGUCAG G@LB@3'-UUU...GUGGU U UGUAC...UAG-5'@LB@ \| \|@LB@ 153 108@LB@@LB@@LB@Energy -13.57 kcal/mol@LB@Hybridization Energy -13.9133 kcal/mol@LB@Unfolding Energy - mRNA 3.57919 kcal/mol@LB@Unfolding Energy - sRNA 0.28482 kcal/mol@LB@@LB@Position - mRNA 153 -- 189@LB@Position - sRNA 109 -- 152@LB@Position Seed - mRNA 31 -- 37@LB@Position Seed - sRNA 172 -- 178@LB@
168	0.01937	0.3812	b4354	yjiY	-11.43	0.145336	99 -- 125	132 -- 159	putative transporter	_____________98__________________________________________________126\n_____________\|___________________________________________________\|\n5'-CUU...UACCU_____UACG_______AACUCU_____CA______A_______A_______AUUUA...ACA-3'\n______________UACUU____CGCGCGU______GGCAA__UC_ACU__CAGGAU_GCGGUCA\n______________\|\|\|\|:____\|:\|:\|:\|______\|\|\|\|\|__\|\|_\|\|\|__\|\|\|:\|\|_\|\|\|\|\|\|\|\n______________AUGAG____GUGUGUA______CCGUU__AG_UGA__GUCUUA_CGCCAGU\n3'-UUU...UGGUU_____UCA________CUACGU_____C___U___AA______A_______AGGGU...UAG-5'\n_____________\|___________________________________________________\|\n_____________160_________________________________________________131\n	119 -- 125	132 -- 138	-39.8751 kcal/mol	13.2469 kcal/mol	12.8104 kcal/mol	98 126@LB@ \| \|@LB@5'-CUU...UACCU UACG AACUCU CA A A AUUUA...ACA-3'@LB@ UACUU CGCGCGU GGCAA UC ACU CAGGAU GCGGUCA@LB@ \|\|\|\|: \|:\|:\|:\| \|\|\|\|\| \|\| \|\|\| \|\|\|:\|\| \|\|\|\|\|\|\|@LB@ AUGAG GUGUGUA CCGUU AG UGA GUCUUA CGCCAGU@LB@3'-UUU...UGGUU UCA CUACGU C U AA A AGGGU...UAG-5'@LB@ \| \|@LB@ 160 131@LB@@LB@@LB@Energy -11.43 kcal/mol@LB@Hybridization Energy -39.8751 kcal/mol@LB@Unfolding Energy - mRNA 13.2469 kcal/mol@LB@Unfolding Energy - sRNA 12.8104 kcal/mol@LB@@LB@Position - mRNA 99 -- 125@LB@Position - sRNA 132 -- 159@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 132 -- 138@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@
170	0.01941	0.3812	b3911	cpxA	-13.13	0.065341	265 -- 299	168 -- 204	sensory histidine kinase in two-component regulatory system with CpxR	_____________264______300\n_____________\|________\|\n5'-UAU...GUUUC________GAUAG...GCC-3'\n______________UGCUUCAU\n______________\|\|\|\|\|\|\|\|\n______________ACGAAGUA\n3'-UUU...GGGGA________G-5'\n_____________\|________\|\n_____________205______167\n	196 -- 202	2 -- 8	-10.3801 kcal/mol	3.0426 kcal/mol	0.709873 kcal/mol	264 300@LB@ \| \|@LB@5'-UAU...GUUUC GAUAG...GCC-3'@LB@ UGCUUCAU@LB@ \|\|\|\|\|\|\|\|@LB@ ACGAAGUA@LB@3'-UUU...GGGGA G-5'@LB@ \| \|@LB@ 205 167@LB@@LB@@LB@Energy -13.13 kcal/mol@LB@Hybridization Energy -10.3801 kcal/mol@LB@Unfolding Energy - mRNA 3.0426 kcal/mol@LB@Unfolding Energy - sRNA 0.709873 kcal/mol@LB@@LB@Position - mRNA 265 -- 299@LB@Position - sRNA 168 -- 204@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 2 -- 8@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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