Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
73	0.01516	0.6177	b0619	citA	-15.44	0.003129	164 -- 175	46 -- 57	sensory histidine kinase in two-component regulatory system with CitB	_____________163__________176\n_____________\|____________\|\n5'-CAU...UACAU____________CUCGG...UCA-3'\n______________CCGUCAAAGAGG\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________GGCAGUUUCUCC\n3'-UUU...AACCG____________UUAAA...ACA-5'\n_____________\|____________\|\n_____________58___________45\n	169 -- 175	46 -- 52	-20.3901 kcal/mol	2.21322 kcal/mol	2.7365 kcal/mol	163 176@LB@ \| \|@LB@5'-CAU...UACAU CUCGG...UCA-3'@LB@ CCGUCAAAGAGG@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ GGCAGUUUCUCC@LB@3'-UUU...AACCG UUAAA...ACA-5'@LB@ \| \|@LB@ 58 45@LB@@LB@@LB@Energy -15.44 kcal/mol@LB@Hybridization Energy -20.3901 kcal/mol@LB@Unfolding Energy - mRNA 2.21322 kcal/mol@LB@Unfolding Energy - sRNA 2.7365 kcal/mol@LB@@LB@Position - mRNA 164 -- 175@LB@Position - sRNA 46 -- 57@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 46 -- 52@LB@
85	0.01786	0.6177	b1427	rimL	-14.01	0.006161	123 -- 133	46 -- 56	ribosomal-protein-L7/L12-serine acetyltransferase	_____________122_________134\n_____________\|___________\|\n5'-GAU...GAGAG___________UGUAA...CCU-3'\n______________CGUCAAAGAGG\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________GCAGUUUCUCC\n3'-UUU...ACCGG___________UUAAA...ACA-5'\n_____________\|___________\|\n_____________57__________45\n	127 -- 133	46 -- 52	-17.3934 kcal/mol	2.45026 kcal/mol	0.93204 kcal/mol	122 134@LB@ \| \|@LB@5'-GAU...GAGAG UGUAA...CCU-3'@LB@ CGUCAAAGAGG@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ GCAGUUUCUCC@LB@3'-UUU...ACCGG UUAAA...ACA-5'@LB@ \| \|@LB@ 57 45@LB@@LB@@LB@Energy -14.01 kcal/mol@LB@Hybridization Energy -17.3934 kcal/mol@LB@Unfolding Energy - mRNA 2.45026 kcal/mol@LB@Unfolding Energy - sRNA 0.93204 kcal/mol@LB@@LB@Position - mRNA 123 -- 133@LB@Position - sRNA 46 -- 56@LB@Position Seed - mRNA 127 -- 133@LB@Position Seed - sRNA 46 -- 52@LB@
87	0.01794	0.6177	b3499	rlmJ	-10.99	0.025859	12 -- 21	46 -- 55	23S rRNA m(6)A2030 methyltransferase SAM-dependent	_____________11_________22\n_____________\|__________\|\n5'-GCG...UCCUG__________UUAAG...AUA-3'\n______________GUUAAAGAGG\n______________\|\|:\|\|\|\|\|\|\|\n______________CAGUUUCUCC\n3'-UUU...CCGGG__________UUAAA...ACA-5'\n_____________\|__________\|\n_____________56_________45\n	15 -- 21	46 -- 52	-14.3615 kcal/mol	2.45195 kcal/mol	0.924411 kcal/mol	11 22@LB@ \| \|@LB@5'-GCG...UCCUG UUAAG...AUA-3'@LB@ GUUAAAGAGG@LB@ \|\|:\|\|\|\|\|\|\|@LB@ CAGUUUCUCC@LB@3'-UUU...CCGGG UUAAA...ACA-5'@LB@ \| \|@LB@ 56 45@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -14.3615 kcal/mol@LB@Unfolding Energy - mRNA 2.45195 kcal/mol@LB@Unfolding Energy - sRNA 0.924411 kcal/mol@LB@@LB@Position - mRNA 12 -- 21@LB@Position - sRNA 46 -- 55@LB@Position Seed - mRNA 15 -- 21@LB@Position Seed - sRNA 46 -- 52@LB@
104	0.02144	0.6177	b2718	hycH	-8.07	0.100760	181 -- 190	46 -- 55	hydrogenase 3 maturation protein	_____________180________191\n_____________\|__________\|\n5'-CAG...AUGUU__________CGCGU...UGG-3'\n______________GUUGAAGAGG\n______________\|\|::\|\|\|\|\|\|\n______________CAGUUUCUCC\n3'-UUU...CCGGG__________UUAAA...ACA-5'\n_____________\|__________\|\n_____________56_________45\n	184 -- 190	46 -- 52	-11.8031 kcal/mol	2.8078 kcal/mol	0.924411 kcal/mol	180 191@LB@ \| \|@LB@5'-CAG...AUGUU CGCGU...UGG-3'@LB@ GUUGAAGAGG@LB@ \|\|::\|\|\|\|\|\|@LB@ CAGUUUCUCC@LB@3'-UUU...CCGGG UUAAA...ACA-5'@LB@ \| \|@LB@ 56 45@LB@@LB@@LB@Energy -8.07 kcal/mol@LB@Hybridization Energy -11.8031 kcal/mol@LB@Unfolding Energy - mRNA 2.8078 kcal/mol@LB@Unfolding Energy - sRNA 0.924411 kcal/mol@LB@@LB@Position - mRNA 181 -- 190@LB@Position - sRNA 46 -- 55@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 46 -- 52@LB@
113	0.02257	0.6177	b0915	lpxK	-7.55	0.127690	105 -- 116	46 -- 56	lipid A 4'kinase	_____________104__________117\n_____________\|____________\|\n5'-GAA...GUGGU_________U__UGUCA...GCU-3'\n______________CGUCGAGGA_GG\n______________\|\|\|\|:\|:\|\|_\|\|\n______________GCAGUUUCU_CC\n3'-UUU...ACCGG____________UUAAA...ACA-5'\n_____________\|____________\|\n_____________57___________45\n	107 -- 113	48 -- 54	-12.734 kcal/mol	4.25329 kcal/mol	0.93204 kcal/mol	104 117@LB@ \| \|@LB@5'-GAA...GUGGU U UGUCA...GCU-3'@LB@ CGUCGAGGA GG@LB@ \|\|\|\|:\|:\|\| \|\|@LB@ GCAGUUUCU CC@LB@3'-UUU...ACCGG UUAAA...ACA-5'@LB@ \| \|@LB@ 57 45@LB@@LB@@LB@Energy -7.55 kcal/mol@LB@Hybridization Energy -12.734 kcal/mol@LB@Unfolding Energy - mRNA 4.25329 kcal/mol@LB@Unfolding Energy - sRNA 0.93204 kcal/mol@LB@@LB@Position - mRNA 105 -- 116@LB@Position - sRNA 46 -- 56@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 48 -- 54@LB@
127	0.0247	0.6177	b3306	rpsH	-8.61	0.078593	53 -- 64	46 -- 57	30S ribosomal subunit protein S8	_____________52___________65\n_____________\|____________\|\n5'-AGC...CGCUG________C___UCGUC...AAG-3'\n______________CCGUCAAA_AGG\n______________\|\|\|\|\|\|\|\|_\|\|\|\n______________GGCAGUUU_UCC\n3'-UUU...AACCG________C___UUAAA...ACA-5'\n_____________\|____________\|\n_____________58___________45\n	54 -- 60	50 -- 56	-14.2597 kcal/mol	2.91134 kcal/mol	2.7365 kcal/mol	52 65@LB@ \| \|@LB@5'-AGC...CGCUG C UCGUC...AAG-3'@LB@ CCGUCAAA AGG@LB@ \|\|\|\|\|\|\|\| \|\|\|@LB@ GGCAGUUU UCC@LB@3'-UUU...AACCG C UUAAA...ACA-5'@LB@ \| \|@LB@ 58 45@LB@@LB@@LB@Energy -8.61 kcal/mol@LB@Hybridization Energy -14.2597 kcal/mol@LB@Unfolding Energy - mRNA 2.91134 kcal/mol@LB@Unfolding Energy - sRNA 2.7365 kcal/mol@LB@@LB@Position - mRNA 53 -- 64@LB@Position - sRNA 46 -- 57@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 50 -- 56@LB@
132	0.02588	0.6177	b3180	yhbY	-5.98	0.252347	290 -- 297	46 -- 53	RNA binding protein associated with pre-50S ribosomal subunits	_____________289______298\n_____________\|________\|\n5'-CUG...UUGAC________UGC-3'\n______________CGAAGGGG\n______________\|:\|\|\|:\|\|\n______________GUUUCUCC\n3'-UUU...GGGCA________UUAAA...ACA-5'\n_____________\|________\|\n_____________54_______45\n	291 -- 297	46 -- 52	-10.2464 kcal/mol	3.35117 kcal/mol	0.910679 kcal/mol	289 298@LB@ \| \|@LB@5'-CUG...UUGAC UGC-3'@LB@ CGAAGGGG@LB@ \|:\|\|\|:\|\|@LB@ GUUUCUCC@LB@3'-UUU...GGGCA UUAAA...ACA-5'@LB@ \| \|@LB@ 54 45@LB@@LB@@LB@Energy -5.98 kcal/mol@LB@Hybridization Energy -10.2464 kcal/mol@LB@Unfolding Energy - mRNA 3.35117 kcal/mol@LB@Unfolding Energy - sRNA 0.910679 kcal/mol@LB@@LB@Position - mRNA 290 -- 297@LB@Position - sRNA 46 -- 53@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 46 -- 52@LB@
162	0.03332	0.6177	b3304	rplR	-8.58	0.079933	170 -- 177	46 -- 53	50S ribosomal subunit protein L18	_____________169______178\n_____________\|________\|\n5'-AUC...CGUAC________CUAAG...GUC-3'\n______________CAAAGAGG\n______________\|\|\|\|\|\|\|\|\n______________GUUUCUCC\n3'-UUU...GGGCA________UUAAA...ACA-5'\n_____________\|________\|\n_____________54_______45\n	171 -- 177	46 -- 52	-11.2869 kcal/mol	1.80103 kcal/mol	0.910679 kcal/mol	169 178@LB@ \| \|@LB@5'-AUC...CGUAC CUAAG...GUC-3'@LB@ CAAAGAGG@LB@ \|\|\|\|\|\|\|\|@LB@ GUUUCUCC@LB@3'-UUU...GGGCA UUAAA...ACA-5'@LB@ \| \|@LB@ 54 45@LB@@LB@@LB@Energy -8.58 kcal/mol@LB@Hybridization Energy -11.2869 kcal/mol@LB@Unfolding Energy - mRNA 1.80103 kcal/mol@LB@Unfolding Energy - sRNA 0.910679 kcal/mol@LB@@LB@Position - mRNA 170 -- 177@LB@Position - sRNA 46 -- 53@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 46 -- 52@LB@
171	0.0346	0.6177	b1865	nudB	-7.50	0.130652	189 -- 196	46 -- 53	dihydroneopterin triphosphate pyrophosphatase	_____________188______197\n_____________\|________\|\n5'-UGA...GUCAA________CAGCG...CCG-3'\n______________CGAAGAGG\n______________\|:\|\|\|\|\|\|\n______________GUUUCUCC\n3'-UUU...GGGCA________UUAAA...ACA-5'\n_____________\|________\|\n_____________54_______45\n	190 -- 196	46 -- 52	-10.7995 kcal/mol	2.39118 kcal/mol	0.910679 kcal/mol	188 197@LB@ \| \|@LB@5'-UGA...GUCAA CAGCG...CCG-3'@LB@ CGAAGAGG@LB@ \|:\|\|\|\|\|\|@LB@ GUUUCUCC@LB@3'-UUU...GGGCA UUAAA...ACA-5'@LB@ \| \|@LB@ 54 45@LB@@LB@@LB@Energy -7.50 kcal/mol@LB@Hybridization Energy -10.7995 kcal/mol@LB@Unfolding Energy - mRNA 2.39118 kcal/mol@LB@Unfolding Energy - sRNA 0.910679 kcal/mol@LB@@LB@Position - mRNA 189 -- 196@LB@Position - sRNA 46 -- 53@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 46 -- 52@LB@
175	0.03585	0.6177	b2028	ugd	-9.30	0.056993	217 -- 248	46 -- 74	UDP-glucose 6-dehydrogenase	_____________216______________________________249\n_____________\|________________________________\|\n5'-GCU...CAUUU______C_G_____GUA___________C___CUUCU...CAC-3'\n______________CCGGUA_U_GCUAU___GGCUUGUCAAA_GGG\n______________\|\|::\|\|_\|_\|\|\|\|\|___\|\|\|::\|\|\|\|\|\|_:\|\|\n______________GGUUAU_A_CGAUA___CCGGGCAGUUU_UCC\n3'-UUU...UUACC________G_____A_____________C___UUAAA...ACA-5'\n_____________\|________________________________\|\n_____________75_______________________________45\n	238 -- 244	50 -- 56	-30.8605 kcal/mol	10.2215 kcal/mol	11.335 kcal/mol	216 249@LB@ \| \|@LB@5'-GCU...CAUUU C G GUA C CUUCU...CAC-3'@LB@ CCGGUA U GCUAU GGCUUGUCAAA GGG@LB@ \|\|::\|\| \| \|\|\|\|\| \|\|\|::\|\|\|\|\|\| :\|\|@LB@ GGUUAU A CGAUA CCGGGCAGUUU UCC@LB@3'-UUU...UUACC G A C UUAAA...ACA-5'@LB@ \| \|@LB@ 75 45@LB@@LB@@LB@Energy -9.30 kcal/mol@LB@Hybridization Energy -30.8605 kcal/mol@LB@Unfolding Energy - mRNA 10.2215 kcal/mol@LB@Unfolding Energy - sRNA 11.335 kcal/mol@LB@@LB@Position - mRNA 217 -- 248@LB@Position - sRNA 46 -- 74@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 50 -- 56@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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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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