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
17	0.0003055	0.06194	stm2694	N/A	-22.95	0.005498	261 -- 295	52 -- 90	Fels-2 prophage protein	_____________260_____________________________________296\n_____________\|_______________________________________\|\n5'-ACG...UAUCA_____________A_G____________AGU________UAUAA-3'\n______________GC___UACGACAA_A_AACGUUACAACC____GCCAAAA\n______________\|\|___:\|\|:\|\|\|\|_\|_\|\|\|:\|:\|\|\|\|\|\|____\|\|\|\|\|\|\|\n______________CG___GUGUUGUU_U_UUGUAGUGUUGG____CGGUUUU\n3'-UUU...GUUAA__UUU________G_G____________CAUU_______CGGGU...UCA-5'\n_____________\|_______________________________________\|\n_____________91______________________________________51\n	289 -- 295	52 -- 58	-35.4487 kcal/mol	2.51857 kcal/mol	14.0353 kcal/mol	260 296@LB@ \| \|@LB@5'-ACG...UAUCA A G AGU UAUAA-3'@LB@ GC UACGACAA A AACGUUACAACC GCCAAAA@LB@ \|\| :\|\|:\|\|\|\| \| \|\|\|:\|:\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ CG GUGUUGUU U UUGUAGUGUUGG CGGUUUU@LB@3'-UUU...GUUAA UUU G G CAUU CGGGU...UCA-5'@LB@ \| \|@LB@ 91 51@LB@@LB@@LB@Energy -22.95 kcal/mol@LB@Hybridization Energy -35.4487 kcal/mol@LB@Unfolding Energy - mRNA 2.51857 kcal/mol@LB@Unfolding Energy - sRNA 14.0353 kcal/mol@LB@@LB@Position - mRNA 261 -- 295@LB@Position - sRNA 52 -- 90@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 52 -- 58@LB@
174	0.009594	0.1945	stm1955	fliZ	-12.61	0.274939	261 -- 282	33 -- 59	flagellar regulatory protein FliZ	_____________260________________283\n_____________\|__________________\|\n5'-GCA...GACUU__________CA______UUGCG...ACC-3'\n______________UAAACACAGC__GACGCA\n______________:\|\|\|\|\|\|\|:\|__:\|\|:\|\|\n______________GUUUGUGUUG__UUGUGU\n3'-UUU...UUAAC__________________UGUAG...UCA-5'\n_____________\|__________________\|\n_____________60_________________32\n	257 -- 263	80 -- 86	-16.495 kcal/mol	1.82497 kcal/mol	3.72065 kcal/mol	260 283@LB@ \| \|@LB@5'-GCA...GACUU CA UUGCG...ACC-3'@LB@ UAAACACAGC GACGCA@LB@ :\|\|\|\|\|\|\|:\| :\|\|:\|\|@LB@ GUUUGUGUUG UUGUGU@LB@3'-UUU...UUAAC UGUAG...UCA-5'@LB@ \| \|@LB@ 60 32@LB@@LB@@LB@Energy -12.61 kcal/mol@LB@Hybridization Energy -16.495 kcal/mol@LB@Unfolding Energy - mRNA 1.82497 kcal/mol@LB@Unfolding Energy - sRNA 3.72065 kcal/mol@LB@@LB@Position - mRNA 261 -- 282@LB@Position - sRNA 33 -- 59@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 80 -- 86@LB@
52	0.001934	0.1324	stm0653	ybeL	-17.18	0.051878	262 -- 299	155 -- 188	similar to E. coli putative alpha helical protein (AAC73744.1); Blastp hit to AAC73744.1 (160 aa) 91% identity in aa 1 - 160	_____________261________________________300\n_____________\|__________________________\|\n5'-AUU...GCGCG________G____G_____G______C-3'\n______________ACAUUGAU_CGCU_GUGGA_CAGGCG\n______________\|\|\|\|\|:\|\|_\|:\|\|_:\|\|\|\|_\|\|\|:\|:\n______________UGUAAUUA_GUGA_UACCU_GUCUGU\n3'-UUU...CACGA__________________________CCCAU...UCA-5'\n_____________\|__________________________\|\n_____________189________________________154\n	275 -- 281	170 -- 176	-23.9532 kcal/mol	9.91713 kcal/mol	4.10825 kcal/mol	261 300@LB@ \| \|@LB@5'-AUU...GCGCG G G G C-3'@LB@ ACAUUGAU CGCU GUGGA CAGGCG@LB@ \|\|\|\|\|:\|\| \|:\|\| :\|\|\|\| \|\|\|:\|:@LB@ UGUAAUUA GUGA UACCU GUCUGU@LB@3'-UUU...CACGA CCCAU...UCA-5'@LB@ \| \|@LB@ 189 154@LB@@LB@@LB@Energy -17.18 kcal/mol@LB@Hybridization Energy -23.9532 kcal/mol@LB@Unfolding Energy - mRNA 9.91713 kcal/mol@LB@Unfolding Energy - sRNA 4.10825 kcal/mol@LB@@LB@Position - mRNA 262 -- 299@LB@Position - sRNA 155 -- 188@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 170 -- 176@LB@
165	0.008886	0.1918	stm0281	N/A	-13.47	0.204933	267 -- 289	36 -- 56	type VI secretion system-associated protein	_____________266______________________________________________290\n_____________\|________________________________________________\|\n5'-UGA...UAAUU____A_____A______A__UAU___C_____UGACC_C_______G_AGUGA...ACC-3'\n______________ACGG_ACGGG_UAAAUG_AU___GAG_UGGAA_____G_GUAGUCU_G\n______________\|\|:\|_\|\|:\|\|_\|\|\|\|\|\|_\|:___:\|\|_\|\|:\|\|_____\|_\|\|\|\|\|\|\|_\|\n______________UGUC_UGUCC_AUUUAC_UG___UUC_ACUUU_____C_CAUCAGA_C\n3'-UUU...AUACC__________C______A__UCC_________UUC___________G_GAUGG...UCA-5'\n_____________\|________________________________________________\|\n_____________57_______________________________________________35\n	219 -- 225	121 -- 127	-29.4304 kcal/mol	8.43831 kcal/mol	11.9516 kcal/mol	266 290@LB@ \| \|@LB@5'-UGA...UAAUU A A A UAU C UGACC C G AGUGA...ACC-3'@LB@ ACGG ACGGG UAAAUG AU GAG UGGAA G GUAGUCU G@LB@ \|\|:\| \|\|:\|\| \|\|\|\|\|\| \|: :\|\| \|\|:\|\| \| \|\|\|\|\|\|\| \|@LB@ UGUC UGUCC AUUUAC UG UUC ACUUU C CAUCAGA C@LB@3'-UUU...AUACC C A UCC UUC G GAUGG...UCA-5'@LB@ \| \|@LB@ 57 35@LB@@LB@@LB@Energy -13.47 kcal/mol@LB@Hybridization Energy -29.4304 kcal/mol@LB@Unfolding Energy - mRNA 8.43831 kcal/mol@LB@Unfolding Energy - sRNA 11.9516 kcal/mol@LB@@LB@Position - mRNA 267 -- 289@LB@Position - sRNA 36 -- 56@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 121 -- 127@LB@
181	0.01001	0.1966	stm2266	apbE	-12.19	0.314808	267 -- 297	62 -- 90	FAD:protein FMN transferase ApbE	_____________266_____________________________298\n_____________\|_______________________________\|\n5'-ACC...AUGAG__UCCCGA______A__________CU____CUC-3'\n______________GC______AACGAC_ACAGCGUCAC__GCCG\n______________\|\|______\|\|\|:\|\|_\|\|\|:\|:\|\|\|\|__:\|\|\|\n______________CG______UUGUUG_UGUUGUAGUG__UGGC\n3'-UUU...GUUAA__UUUGUG_________________U_____AUUCG...UCA-5'\n_____________\|_______________________________\|\n_____________91______________________________61\n	285 -- 291	67 -- 73	-27.9543 kcal/mol	7.52451 kcal/mol	8.62576 kcal/mol	266 298@LB@ \| \|@LB@5'-ACC...AUGAG UCCCGA A CU CUC-3'@LB@ GC AACGAC ACAGCGUCAC GCCG@LB@ \|\| \|\|\|:\|\| \|\|\|:\|:\|\|\|\| :\|\|\|@LB@ CG UUGUUG UGUUGUAGUG UGGC@LB@3'-UUU...GUUAA UUUGUG U AUUCG...UCA-5'@LB@ \| \|@LB@ 91 61@LB@@LB@@LB@Energy -12.19 kcal/mol@LB@Hybridization Energy -27.9543 kcal/mol@LB@Unfolding Energy - mRNA 7.52451 kcal/mol@LB@Unfolding Energy - sRNA 8.62576 kcal/mol@LB@@LB@Position - mRNA 267 -- 297@LB@Position - sRNA 62 -- 90@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 67 -- 73@LB@
78	0.003685	0.1596	stm0423	ispA	-20.49	0.014403	269 -- 289	38 -- 58	(2E 6E)-farnesyl diphosphate synthase	_____________268____________________290\n_____________\|______________________\|\n5'-UGA...AUCGC____CU_____UU_________UCCCG...UCG-3'\n______________GCCA___GCCC__UCAGAACAC\n______________\|\|\|\|___\|\|\|\|__\|\|\|\|\|\|\|\|\|\n______________CGGU___CGGG__AGUCUUGUG\n3'-UUU...GCAUU____UUU____U__________CGUAA...UCA-5'\n_____________\|______________________\|\n_____________59_____________________37\n	281 -- 287	40 -- 46	-28.5082 kcal/mol	2.40221 kcal/mol	13.7699 kcal/mol	268 290@LB@ \| \|@LB@5'-UGA...AUCGC CU UU UCCCG...UCG-3'@LB@ GCCA GCCC UCAGAACAC@LB@ \|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ CGGU CGGG AGUCUUGUG@LB@3'-UUU...GCAUU UUU U CGUAA...UCA-5'@LB@ \| \|@LB@ 59 37@LB@@LB@@LB@Energy -20.49 kcal/mol@LB@Hybridization Energy -28.5082 kcal/mol@LB@Unfolding Energy - mRNA 2.40221 kcal/mol@LB@Unfolding Energy - sRNA 13.7699 kcal/mol@LB@@LB@Position - mRNA 269 -- 289@LB@Position - sRNA 38 -- 58@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 40 -- 46@LB@
113	0.005549	0.1728	stm2948	cysJ	-13.61	0.194760	269 -- 298	56 -- 85	sulfite reductase [NADPH] flavoprotein subunit alpha	_____________268_______________________299\n_____________\|_________________________\|\n5'-GUU...CCGCU____UUACUG_______________UGACG...UUG-3'\n______________UUGC______GAACAUAACGACGCA\n______________\|\|\|\|______:\|\|\|\|:\|\|\|:\|\|:\|\|\n______________AACG______UUUGUGUUGUUGUGU\n3'-UUU...UGGUU_________________________UGUAG...UCA-5'\n_____________\|_________________________\|\n_____________86________________________55\n	195 -- 201	74 -- 80	-20.7575 kcal/mol	3.67756 kcal/mol	3.73922 kcal/mol	268 299@LB@ \| \|@LB@5'-GUU...CCGCU UUACUG UGACG...UUG-3'@LB@ UUGC GAACAUAACGACGCA@LB@ \|\|\|\| :\|\|\|\|:\|\|\|:\|\|:\|\|@LB@ AACG UUUGUGUUGUUGUGU@LB@3'-UUU...UGGUU UGUAG...UCA-5'@LB@ \| \|@LB@ 86 55@LB@@LB@@LB@Energy -13.61 kcal/mol@LB@Hybridization Energy -20.7575 kcal/mol@LB@Unfolding Energy - mRNA 3.67756 kcal/mol@LB@Unfolding Energy - sRNA 3.73922 kcal/mol@LB@@LB@Position - mRNA 269 -- 298@LB@Position - sRNA 56 -- 85@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 74 -- 80@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@
23	0.0005914	0.08814	stm3466	crp	-13.97	0.171291	272 -- 288	36 -- 50	transcriptional regulator Crp	_____________271_______________________________289\n_____________\|_________________________________\|\n5'-ACG...CGAAA______CUAAA________________C_____UAAUA...AGG-3'\n______________GCUAUG_____ACAGACA____AGAUG_UACAG\n______________:\|\|\|\|\|_____\|\|\|\|\|\|\|____\|:\|\|\|_\|\|\|\|\|\n______________UGAUAC_____UGUCUGU____UUUAC_AUGUC\n3'-UUU...AUUAG______C___________CCCA___________CUUCA...UCA-5'\n_____________\|_________________________________\|\n_____________51________________________________35\n	21 -- 27	155 -- 161	-20.3438 kcal/mol	4.64329 kcal/mol	5.58455 kcal/mol	271 289@LB@ \| \|@LB@5'-ACG...CGAAA CUAAA C UAAUA...AGG-3'@LB@ GCUAUG ACAGACA AGAUG UACAG@LB@ :\|\|\|\|\| \|\|\|\|\|\|\| \|:\|\|\| \|\|\|\|\|@LB@ UGAUAC UGUCUGU UUUAC AUGUC@LB@3'-UUU...AUUAG C CCCA CUUCA...UCA-5'@LB@ \| \|@LB@ 51 35@LB@@LB@@LB@Energy -13.97 kcal/mol@LB@Hybridization Energy -20.3438 kcal/mol@LB@Unfolding Energy - mRNA 4.64329 kcal/mol@LB@Unfolding Energy - sRNA 5.58455 kcal/mol@LB@@LB@Position - mRNA 272 -- 288@LB@Position - sRNA 36 -- 50@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 155 -- 161@LB@
96	0.004303	0.1596	stm4243	yjbN	-11.74	0.363864	272 -- 280	155 -- 163	tRNA dihydrouridine(20/20a) synthase DusA	_____________271______________________________281\n_____________\|________________________________\|\n5'-UUA...UUAAU___AC_________C____A_____CCU____GGCAG...GUU-3'\n______________GGG____UGUACGG_GAAG_UGAAA___GGGG\n______________\|\|\|____\|\|\|\|\|:\|_\|\|\|\|_\|\|\|\|\|___:\|\|\|\n______________CCC____ACAUGUC_CUUC_ACUUU___UCCC\n3'-UUU...UCUGU___AUUU__________________U______AUCAG...UCA-5'\n_____________\|________________________________\|\n_____________164______________________________154\n	58 -- 64	141 -- 147	-26.0653 kcal/mol	8.12251 kcal/mol	7.07058 kcal/mol	271 281@LB@ \| \|@LB@5'-UUA...UUAAU AC C A CCU GGCAG...GUU-3'@LB@ GGG UGUACGG GAAG UGAAA GGGG@LB@ \|\|\| \|\|\|\|\|:\| \|\|\|\| \|\|\|\|\| :\|\|\|@LB@ CCC ACAUGUC CUUC ACUUU UCCC@LB@3'-UUU...UCUGU AUUU U AUCAG...UCA-5'@LB@ \| \|@LB@ 164 154@LB@@LB@@LB@Energy -11.74 kcal/mol@LB@Hybridization Energy -26.0653 kcal/mol@LB@Unfolding Energy - mRNA 8.12251 kcal/mol@LB@Unfolding Energy - sRNA 7.07058 kcal/mol@LB@@LB@Position - mRNA 272 -- 280@LB@Position - sRNA 155 -- 163@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 141 -- 147@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

Use the following button if you want to resubmit the job with altered input or parameterization:

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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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