Input and runtime details for job 3202356 (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 3202356 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:02 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:35 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:03:47 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:03:55 CET 2018
	Job Completed		@ Sat Feb 17 02:04:28 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3202356&toolName=CopraRNA ( 30 days expiry )

Description of the job

GcvB

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_003197 NC_003277 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

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
122	0.00604	0.1758	stm2353	hisQ	-14.65	0.134227	190 -- 212	140 -- 163	amino acid ABC transporter permease	_____________189______________________213\n_____________\|________________________\|\n5'-GAU...CAACA________UGCAUGU_________UUUUC...UCG-3'\n______________GGACAGGC________UGUACGGG\n______________\|\|\|\|\|\|:\|________\|\|\|\|\|:\|\|\n______________CCUGUCUG________ACAUGUCC\n3'-UUU...UGAUA________UCCCAUUU________UUCAC...UCA-5'\n_____________\|________________________\|\n_____________164______________________139\n	206 -- 212	140 -- 146	-25.7393 kcal/mol	6.65037 kcal/mol	3.70771 kcal/mol	189 213@LB@ \| \|@LB@5'-GAU...CAACA UGCAUGU UUUUC...UCG-3'@LB@ GGACAGGC UGUACGGG@LB@ \|\|\|\|\|\|:\| \|\|\|\|\|:\|\|@LB@ CCUGUCUG ACAUGUCC@LB@3'-UUU...UGAUA UCCCAUUU UUCAC...UCA-5'@LB@ \| \|@LB@ 164 139@LB@@LB@@LB@Energy -14.65 kcal/mol@LB@Hybridization Energy -25.7393 kcal/mol@LB@Unfolding Energy - mRNA 6.65037 kcal/mol@LB@Unfolding Energy - sRNA 3.70771 kcal/mol@LB@@LB@Position - mRNA 190 -- 212@LB@Position - sRNA 140 -- 163@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 140 -- 146@LB@
2	2.663e-05	0.04123	stm2355	argT	-17.69	0.042680	144 -- 202	34 -- 91	histidine ABC transporter substrate-binding protein HisJ	_____________143____________________203\n_____________\|______________________\|\n5'-UUA...AAGUC_________________C____AAAAC...AUA-3'\n______________UGCAAACAC_ACAACGC_ACGU\n______________\|\|\|\|\|\|\|\|\|_\|\|\|\|\|:\|_\|\|:\|\n______________ACGUUUGUG_UGUUGUG_UGUA\n3'-UUU...GGUUA_________U_______U____GUGUU...UCA-5'\n_____________\|______________________\|\n_____________92_____________________33\n	153 -- 159	75 -- 81	-25.653 kcal/mol	2.98604 kcal/mol	4.21448 kcal/mol	143 203@LB@ \| \|@LB@5'-UUA...AAGUC C AAAAC...AUA-3'@LB@ UGCAAACAC ACAACGC ACGU@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|\|:\| \|\|:\|@LB@ ACGUUUGUG UGUUGUG UGUA@LB@3'-UUU...GGUUA U U GUGUU...UCA-5'@LB@ \| \|@LB@ 92 33@LB@@LB@@LB@Energy -17.69 kcal/mol@LB@Hybridization Energy -25.653 kcal/mol@LB@Unfolding Energy - mRNA 2.98604 kcal/mol@LB@Unfolding Energy - sRNA 4.21448 kcal/mol@LB@@LB@Position - mRNA 144 -- 202@LB@Position - sRNA 34 -- 91@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 75 -- 81@LB@
151	0.00796	0.1845	stm2365	folC	-10.71	0.491716	269 -- 300	50 -- 78	bifunctional tetrahydrofolate synthase/dihydrofolate synthase	_____________268__________301\n_____________\|____________\|\n5'-CCG...CGGCG____A_______UCUGA...AGC-3'\n______________CCGG_UCAGGAG\n______________\|\|\|\|_\|\|\|\|\|\|:\n______________GGCC_AGUCCUU\n3'-UUU...AGCAA____G_______CA-5'\n_____________\|____________\|\n_____________79___________49\n	115 -- 121	3 -- 9	-17.3652 kcal/mol	5.30633 kcal/mol	4.72771 kcal/mol	268 301@LB@ \| \|@LB@5'-CCG...CGGCG A UCUGA...AGC-3'@LB@ CCGG UCAGGAG@LB@ \|\|\|\| \|\|\|\|\|\|:@LB@ GGCC AGUCCUU@LB@3'-UUU...AGCAA G CA-5'@LB@ \| \|@LB@ 79 49@LB@@LB@@LB@Energy -10.71 kcal/mol@LB@Hybridization Energy -17.3652 kcal/mol@LB@Unfolding Energy - mRNA 5.30633 kcal/mol@LB@Unfolding Energy - sRNA 4.72771 kcal/mol@LB@@LB@Position - mRNA 269 -- 300@LB@Position - sRNA 50 -- 78@LB@Position Seed - mRNA 115 -- 121@LB@Position Seed - sRNA 3 -- 9@LB@
20	0.0004512	0.08034	stm2384	aroC	-21.00	0.011794	171 -- 223	39 -- 90	chorismate synthase	_____________170___________________224\n_____________\|_____________________\|\n5'-GUU...AACAC______G________G_____GGAGC...GCA-3'\n______________GCAAAC_ACAACAAC_AUAAC\n______________\|\|\|\|\|\|_\|\|\|\|\|\|\|\|_\|:\|\|\|\n______________CGUUUG_UGUUGUUG_UGUUG\n3'-UUU...GUUAA_____________________UAGUG...UCA-5'\n_____________\|_____________________\|\n_____________91____________________38\n	179 -- 185	77 -- 83	-22.4295 kcal/mol	1.97696 kcal/mol	3.80362 kcal/mol	170 224@LB@ \| \|@LB@5'-GUU...AACAC G G GGAGC...GCA-3'@LB@ GCAAAC ACAACAAC AUAAC@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|\| \|:\|\|\|@LB@ CGUUUG UGUUGUUG UGUUG@LB@3'-UUU...GUUAA UAGUG...UCA-5'@LB@ \| \|@LB@ 91 38@LB@@LB@@LB@Energy -21.00 kcal/mol@LB@Hybridization Energy -22.4295 kcal/mol@LB@Unfolding Energy - mRNA 1.97696 kcal/mol@LB@Unfolding Energy - sRNA 3.80362 kcal/mol@LB@@LB@Position - mRNA 171 -- 223@LB@Position - sRNA 39 -- 90@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 77 -- 83@LB@
37	0.001263	0.1215	stm2511	guaB	-22.14	0.007548	255 -- 298	35 -- 73	IMP dehydrogenase	_____________254___________________________________________299\n_____________\|_____________________________________________\|\n5'-GGC...UUCCC_______UCC_____UUU______UACU___G___UC________GU-3'\n______________GC_UCAC___ACCGU___GCCGAA____GCC_AUC__AGCACGCA\n______________:\|_\|\|\|\|___\|\|\|\|\|___\|\|\|:\|\|____\|\|\|_\|\|\|__\|:\|\|\|\|\|\|\n______________UG_AGUG___UGGCA___CGGUUU____CGG_UAG__UUGUGCGU\n3'-UUU...UGUGU__U____U_______UU_______U______G___UC________AAGGC...UCA-5'\n_____________\|_____________________________________________\|\n_____________74____________________________________________34\n	292 -- 298	35 -- 41	-39.0524 kcal/mol	5.99157 kcal/mol	19.7557 kcal/mol	254 299@LB@ \| \|@LB@5'-GGC...UUCCC UCC UUU UACU G UC GU-3'@LB@ GC UCAC ACCGU GCCGAA GCC AUC AGCACGCA@LB@ :\| \|\|\|\| \|\|\|\|\| \|\|\|:\|\| \|\|\| \|\|\| \|:\|\|\|\|\|\|@LB@ UG AGUG UGGCA CGGUUU CGG UAG UUGUGCGU@LB@3'-UUU...UGUGU U U UU U G UC AAGGC...UCA-5'@LB@ \| \|@LB@ 74 34@LB@@LB@@LB@Energy -22.14 kcal/mol@LB@Hybridization Energy -39.0524 kcal/mol@LB@Unfolding Energy - mRNA 5.99157 kcal/mol@LB@Unfolding Energy - sRNA 19.7557 kcal/mol@LB@@LB@Position - mRNA 255 -- 298@LB@Position - sRNA 35 -- 73@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 35 -- 41@LB@
153	0.008123	0.1845	stm2512	xseA	-14.57	0.138273	215 -- 252	42 -- 82	exodeoxyribonuclease VII large subunit	_____________214________253\n_____________\|__________\|\n5'-CGU...UUUUU__________GCCUU...GCG-3'\n______________ACCGUAAGCC\n______________\|\|\|\|\|\|\|\|\|\|\n______________UGGCAUUCGG\n3'-UUU...AGUGU__________UUUUC...UCA-5'\n_____________\|__________\|\n_____________83_________41\n	234 -- 240	56 -- 62	-17.1871 kcal/mol	1.1981 kcal/mol	7.48121 kcal/mol	214 253@LB@ \| \|@LB@5'-CGU...UUUUU GCCUU...GCG-3'@LB@ ACCGUAAGCC@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UGGCAUUCGG@LB@3'-UUU...AGUGU UUUUC...UCA-5'@LB@ \| \|@LB@ 83 41@LB@@LB@@LB@Energy -14.57 kcal/mol@LB@Hybridization Energy -17.1871 kcal/mol@LB@Unfolding Energy - mRNA 1.1981 kcal/mol@LB@Unfolding Energy - sRNA 7.48121 kcal/mol@LB@@LB@Position - mRNA 215 -- 252@LB@Position - sRNA 42 -- 82@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 56 -- 62@LB@
150	0.007945	0.1845	stm2555	glyA	-15.42	0.100951	252 -- 282	137 -- 168	serine hydroxymethyltransferase	_____________251_________________________________283\n_____________\|___________________________________\|\n5'-CAC...GGCAG________________AA________GUC______AGCAC...UCG-3'\n______________GCUAUGGA___GCAGG__AAA_GUAC___AGGAAG\n______________:\|\|\|\|\|\|\|___:\|\|\|\|__\|\|\|_\|\|\|\|___\|\|\|\|\|\|\n______________UGAUACCU___UGUCC__UUU_CAUG___UCCUUC\n3'-UUU...AUUAG________GUC_____CA___A_____________ACUUU...UCA-5'\n_____________\|___________________________________\|\n_____________169_________________________________136\n	253 -- 259	161 -- 167	-28.2568 kcal/mol	5.17684 kcal/mol	6.91101 kcal/mol	251 283@LB@ \| \|@LB@5'-CAC...GGCAG AA GUC AGCAC...UCG-3'@LB@ GCUAUGGA GCAGG AAA GUAC AGGAAG@LB@ :\|\|\|\|\|\|\| :\|\|\|\| \|\|\| \|\|\|\| \|\|\|\|\|\|@LB@ UGAUACCU UGUCC UUU CAUG UCCUUC@LB@3'-UUU...AUUAG GUC CA A ACUUU...UCA-5'@LB@ \| \|@LB@ 169 136@LB@@LB@@LB@Energy -15.42 kcal/mol@LB@Hybridization Energy -28.2568 kcal/mol@LB@Unfolding Energy - mRNA 5.17684 kcal/mol@LB@Unfolding Energy - sRNA 6.91101 kcal/mol@LB@@LB@Position - mRNA 252 -- 282@LB@Position - sRNA 137 -- 168@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 161 -- 167@LB@
117	0.005749	0.1738	stm2562	yfhA	-19.31	0.022783	16 -- 66	47 -- 100	two-component system response regulator GlrR	_____________15____________67\n_____________\|_____________\|\n5'-CUG...AGGCC_____________UCGAU...UCG-3'\n______________UUGCAAACGCAGC\n______________\|\|\|\|\|\|\|\|:\|\|:\|\n______________AACGUUUGUGUUG\n3'-UUU...UGGUU_____________UUGUG...UCA-5'\n_____________\|_____________\|\n_____________101___________46\n	28 -- 34	80 -- 86	-18.759 kcal/mol	3.6583 kcal/mol	3.5889 kcal/mol	15 67@LB@ \| \|@LB@5'-CUG...AGGCC UCGAU...UCG-3'@LB@ UUGCAAACGCAGC@LB@ \|\|\|\|\|\|\|\|:\|\|:\|@LB@ AACGUUUGUGUUG@LB@3'-UUU...UGGUU UUGUG...UCA-5'@LB@ \| \|@LB@ 101 46@LB@@LB@@LB@Energy -19.31 kcal/mol@LB@Hybridization Energy -18.759 kcal/mol@LB@Unfolding Energy - mRNA 3.6583 kcal/mol@LB@Unfolding Energy - sRNA 3.5889 kcal/mol@LB@@LB@Position - mRNA 16 -- 66@LB@Position - sRNA 47 -- 100@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 80 -- 86@LB@
192	0.01067	0.197	stm2650	yfiP	-13.22	0.223534	188 -- 232	36 -- 90	DTW domain-containing protein	_____________187_________________________233\n_____________\|___________________________\|\n5'-UCA...UCUCC________UUUCUAUGACC________UGUCC...GCU-3'\n______________GCAAACGC___________AAUAACGC\n______________\|\|\|\|\|\|:\|___________\|\|:\|\|\|:\|\n______________CGUUUGUG___________UUGUUGUG\n3'-UUU...GUUAA___________________________UUGUA...UCA-5'\n_____________\|___________________________\|\n_____________91__________________________35\n	208 -- 214	75 -- 81	-16.7007 kcal/mol	3.95203 kcal/mol	3.72363 kcal/mol	187 233@LB@ \| \|@LB@5'-UCA...UCUCC UUUCUAUGACC UGUCC...GCU-3'@LB@ GCAAACGC AAUAACGC@LB@ \|\|\|\|\|\|:\| \|\|:\|\|\|:\|@LB@ CGUUUGUG UUGUUGUG@LB@3'-UUU...GUUAA UUGUA...UCA-5'@LB@ \| \|@LB@ 91 35@LB@@LB@@LB@Energy -13.22 kcal/mol@LB@Hybridization Energy -16.7007 kcal/mol@LB@Unfolding Energy - mRNA 3.95203 kcal/mol@LB@Unfolding Energy - sRNA 3.72363 kcal/mol@LB@@LB@Position - mRNA 188 -- 232@LB@Position - sRNA 36 -- 90@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 75 -- 81@LB@
88	0.00402	0.1596	stm2651	yfiQ	-16.02	0.080775	116 -- 159	50 -- 88	protein acetyltransferase	_____________115__________________________160\n_____________\|____________________________\|\n5'-CAA...AGGAA__________UCCGGGA___________AUAAA...GUA-3'\n______________AAACGCAACA_______AACGUCACAGC\n______________\|\|\|\|:\|\|\|\|\|_______\|\|\|:\|\|\|\|\|:\|\n______________UUUGUGUUGU_______UUGUAGUGUUG\n3'-UUU...UAACG__________UGUG______________GCAUU...UCA-5'\n_____________\|____________________________\|\n_____________89___________________________49\n	137 -- 143	64 -- 70	-25.6269 kcal/mol	4.45838 kcal/mol	7.90699 kcal/mol	115 160@LB@ \| \|@LB@5'-CAA...AGGAA UCCGGGA AUAAA...GUA-3'@LB@ AAACGCAACA AACGUCACAGC@LB@ \|\|\|\|:\|\|\|\|\| \|\|\|:\|\|\|\|\|:\|@LB@ UUUGUGUUGU UUGUAGUGUUG@LB@3'-UUU...UAACG UGUG GCAUU...UCA-5'@LB@ \| \|@LB@ 89 49@LB@@LB@@LB@Energy -16.02 kcal/mol@LB@Hybridization Energy -25.6269 kcal/mol@LB@Unfolding Energy - mRNA 4.45838 kcal/mol@LB@Unfolding Energy - sRNA 7.90699 kcal/mol@LB@@LB@Position - mRNA 116 -- 159@LB@Position - sRNA 50 -- 88@LB@Position Seed - mRNA 137 -- 143@LB@Position Seed - sRNA 64 -- 70@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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