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	Additional homologs
12	0.0002098	0.05681	stm3344	rpsI	-21.57	0.009451	131 -- 172	57 -- 102	30S ribosomal protein S9		_____________130__________________________173\n_____________\|____________________________\|\n5'-GUG...GGCAA__________C________CA_______CAAGU...GUU-3'\n______________CGAGCACAAC_ACGCGGCA__GCAACCG\n______________\|:\|:\|\|\|\|\|\|_\|\|:\|::\|\|__:\|\|\|\|\|\|\n______________GUUUGUGUUG_UGUGUUGU__UGUUGGC\n3'-UUU...UUAAC__________U________AG_______AUUCG...UCA-5'\n_____________\|____________________________\|\n_____________103__________________________56\n	161 -- 167	62 -- 68	-36.1701 kcal/mol	9.00411 kcal/mol	8.61223 kcal/mol	130 173@LB@ \| \|@LB@5'-GUG...GGCAA C CA CAAGU...GUU-3'@LB@ CGAGCACAAC ACGCGGCA GCAACCG@LB@ \|:\|:\|\|\|\|\|\| \|\|:\|::\|\| :\|\|\|\|\|\|@LB@ GUUUGUGUUG UGUGUUGU UGUUGGC@LB@3'-UUU...UUAAC U AG AUUCG...UCA-5'@LB@ \| \|@LB@ 103 56@LB@@LB@@LB@Energy -21.57 kcal/mol@LB@Hybridization Energy -36.1701 kcal/mol@LB@Unfolding Energy - mRNA 9.00411 kcal/mol@LB@Unfolding Energy - sRNA 8.61223 kcal/mol@LB@@LB@Position - mRNA 131 -- 172@LB@Position - sRNA 57 -- 102@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 62 -- 68@LB@
87	0.004009	0.1596	stm2067	sbcB	-11.70	0.367652	220 -- 292	35 -- 90	exodeoxyribonuclease I		_____________219_____________________293\n_____________\|_______________________\|\n5'-AUU...AUGUA______U________________AUUGG...CCG-3'\n______________CGAACA_UAGCA__ACAAUAUCA\n______________\|:\|\|\|\|_:\|:\|\|__\|\|\|\|:\|\|\|\|\n______________GUUUGU_GUUGU__UGUUGUAGU\n3'-UUU...UUAAC____________UG_________GUUGG...UCA-5'\n_____________\|_______________________\|\n_____________91______________________34\n	110 -- 116	68 -- 74	-17.8808 kcal/mol	2.08887 kcal/mol	5.27986 kcal/mol	219 293@LB@ \| \|@LB@5'-AUU...AUGUA U AUUGG...CCG-3'@LB@ CGAACA UAGCA ACAAUAUCA@LB@ \|:\|\|\|\| :\|:\|\| \|\|\|\|:\|\|\|\|@LB@ GUUUGU GUUGU UGUUGUAGU@LB@3'-UUU...UUAAC UG GUUGG...UCA-5'@LB@ \| \|@LB@ 91 34@LB@@LB@@LB@Energy -11.70 kcal/mol@LB@Hybridization Energy -17.8808 kcal/mol@LB@Unfolding Energy - mRNA 2.08887 kcal/mol@LB@Unfolding Energy - sRNA 5.27986 kcal/mol@LB@@LB@Position - mRNA 220 -- 292@LB@Position - sRNA 35 -- 90@LB@Position Seed - mRNA 110 -- 116@LB@Position Seed - sRNA 68 -- 74@LB@
28	0.0007333	0.08814	stm0376	sbmA	-15.26	0.107034	68 -- 102	55 -- 90	peptide transporter		_____________67______________________________103\n_____________\|_______________________________\|\n5'-GCU...AGAAA_______UA____U______GUAG_______UGCCU...AUU-3'\n______________UGCGAAC__AGCG_CACAAC____GUCACAA\n______________\|\|\|:\|\|\|__\|:\|:_\|\|\|\|\|\|____:\|\|\|\|\|\|\n______________ACGUUUG__UUGU_GUGUUG____UAGUGUU\n3'-UUU...GGUUA_______UG____U_________________GGCAU...UCA-5'\n_____________\|_______________________________\|\n_____________91______________________________54\n	99 -- 105	65 -- 71	-26.4432 kcal/mol	7.11088 kcal/mol	6.59083 kcal/mol	67 103@LB@ \| \|@LB@5'-GCU...AGAAA UA U GUAG UGCCU...AUU-3'@LB@ UGCGAAC AGCG CACAAC GUCACAA@LB@ \|\|\|:\|\|\| \|:\|: \|\|\|\|\|\| :\|\|\|\|\|\|@LB@ ACGUUUG UUGU GUGUUG UAGUGUU@LB@3'-UUU...GGUUA UG U GGCAU...UCA-5'@LB@ \| \|@LB@ 91 54@LB@@LB@@LB@Energy -15.26 kcal/mol@LB@Hybridization Energy -26.4432 kcal/mol@LB@Unfolding Energy - mRNA 7.11088 kcal/mol@LB@Unfolding Energy - sRNA 6.59083 kcal/mol@LB@@LB@Position - mRNA 68 -- 102@LB@Position - sRNA 55 -- 90@LB@Position Seed - mRNA 99 -- 105@LB@Position Seed - sRNA 65 -- 71@LB@
93	0.004254	0.1596	stm0408	secF	-18.22	0.034847	7 -- 64	39 -- 91	protein-export membrane protein SecF		_____________6______________________________________65\n_____________\|______________________________________\|\n5'-CUU...GCACA_G__U____UGUUG______UA________________AGUCU...UGC-3'\n______________G_AA_ACAC_____AACAAC__AAC__CACGGCCGUAA\n______________\|_\|\|_\|\|\|\|_____\|\|\|\|\|\|__\|\|\|__\|\|\|::\|\|\|\|\|\|\n______________C_UU_UGUG_____UUGUUG__UUG__GUGUUGGCAUU\n3'-UUU...GUUAA_G__________________UG___UA___________CGGUU...UCA-5'\n_____________\|______________________________________\|\n_____________92_____________________________________38\n	238 -- 244	59 -- 65	-26.2573 kcal/mol	3.95572 kcal/mol	10.1648 kcal/mol	6 65@LB@ \| \|@LB@5'-CUU...GCACA G U UGUUG UA AGUCU...UGC-3'@LB@ G AA ACAC AACAAC AAC CACGGCCGUAA@LB@ \| \|\| \|\|\|\| \|\|\|\|\|\| \|\|\| \|\|\|::\|\|\|\|\|\|@LB@ C UU UGUG UUGUUG UUG GUGUUGGCAUU@LB@3'-UUU...GUUAA G UG UA CGGUU...UCA-5'@LB@ \| \|@LB@ 92 38@LB@@LB@@LB@Energy -18.22 kcal/mol@LB@Hybridization Energy -26.2573 kcal/mol@LB@Unfolding Energy - mRNA 3.95572 kcal/mol@LB@Unfolding Energy - sRNA 10.1648 kcal/mol@LB@@LB@Position - mRNA 7 -- 64@LB@Position - sRNA 39 -- 91@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 59 -- 65@LB@
40	0.001409	0.1215	stm4578	serB	-16.00	0.081343	27 -- 78	37 -- 87	phosphoserine phosphatase SerB		_____________26___________________79\n_____________\|____________________\|\n5'-CUG...CAGUG________G___________GACUG...ACC-3'\n______________UG_AGACA_AACAAUACAAU\n______________\|\|_\|:\|\|\|_\|\|\|\|\|:\|\|\|\|:\n______________AC_UUUGU_UUGUUGUGUUG\n3'-UUU...GGUUA__G_____G___________UAGUG...UCA-5'\n_____________\|____________________\|\n_____________88___________________36\n	36 -- 42	72 -- 78	-19.1859 kcal/mol	2.1479 kcal/mol	3.80548 kcal/mol	26 79@LB@ \| \|@LB@5'-CUG...CAGUG G GACUG...ACC-3'@LB@ UG AGACA AACAAUACAAU@LB@ \|\| \|:\|\|\| \|\|\|\|\|:\|\|\|\|:@LB@ AC UUUGU UUGUUGUGUUG@LB@3'-UUU...GGUUA G G UAGUG...UCA-5'@LB@ \| \|@LB@ 88 36@LB@@LB@@LB@Energy -16.00 kcal/mol@LB@Hybridization Energy -19.1859 kcal/mol@LB@Unfolding Energy - mRNA 2.1479 kcal/mol@LB@Unfolding Energy - sRNA 3.80548 kcal/mol@LB@@LB@Position - mRNA 27 -- 78@LB@Position - sRNA 37 -- 87@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 72 -- 78@LB@
69	0.003278	0.1596	stm3675	sgbH	-16.55	0.065932	154 -- 200	33 -- 93	3-keto-L-gulonate-6-phosphate decarboxylase		_____________153_______________________201\n_____________\|_________________________\|\n5'-UUC...CAGUC__G_____GCC______________CCUGC...AGG-3'\n______________UG_AAGCA___CAACGCGAUGUCGC\n______________\|\|_\|\|:\|\|___\|\|\|\|:\|:\|::\|\|:\|\n______________AC_UUUGU___GUUGUGUUGUAGUG\n3'-UUU...GGUUA__G_____GUU______________UUGGC...UCA-5'\n_____________\|_________________________\|\n_____________94________________________32\n	258 -- 264	71 -- 77	-24.2274 kcal/mol	7.7572 kcal/mol	5.6854 kcal/mol	153 201@LB@ \| \|@LB@5'-UUC...CAGUC G GCC CCUGC...AGG-3'@LB@ UG AAGCA CAACGCGAUGUCGC@LB@ \|\| \|\|:\|\| \|\|\|\|:\|:\|::\|\|:\|@LB@ AC UUUGU GUUGUGUUGUAGUG@LB@3'-UUU...GGUUA G GUU UUGGC...UCA-5'@LB@ \| \|@LB@ 94 32@LB@@LB@@LB@Energy -16.55 kcal/mol@LB@Hybridization Energy -24.2274 kcal/mol@LB@Unfolding Energy - mRNA 7.7572 kcal/mol@LB@Unfolding Energy - sRNA 5.6854 kcal/mol@LB@@LB@Position - mRNA 154 -- 200@LB@Position - sRNA 33 -- 93@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 71 -- 77@LB@
70	0.003306	0.1596	stm2688	smpB	-12.25	0.308628	191 -- 230	36 -- 77	SsrA-binding protein		_____________190_________________231\n_____________\|___________________\|\n5'-AAU...GCAUA____UUCC__U________AUCGU...GUC-3'\n______________GCAA____CA_CAACAUAA\n______________\|\|\|\|____\|\|_\|\|\|\|\|:\|\|\n______________CGUU____GU_GUUGUGUU\n3'-UUU...GUUAA____UGU___U________GUAGU...UCA-5'\n_____________\|___________________\|\n_____________78__________________35\n	26 -- 32	73 -- 79	-12.551 kcal/mol	1.44298 kcal/mol	3.77104 kcal/mol	190 231@LB@ \| \|@LB@5'-AAU...GCAUA UUCC U AUCGU...GUC-3'@LB@ GCAA CA CAACAUAA@LB@ \|\|\|\| \|\| \|\|\|\|\|:\|\|@LB@ CGUU GU GUUGUGUU@LB@3'-UUU...GUUAA UGU U GUAGU...UCA-5'@LB@ \| \|@LB@ 78 35@LB@@LB@@LB@Energy -12.25 kcal/mol@LB@Hybridization Energy -12.551 kcal/mol@LB@Unfolding Energy - mRNA 1.44298 kcal/mol@LB@Unfolding Energy - sRNA 3.77104 kcal/mol@LB@@LB@Position - mRNA 191 -- 230@LB@Position - sRNA 36 -- 77@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 73 -- 79@LB@
135	0.006796	0.1774	stm1044	sodC	-14.39	0.147293	208 -- 244	43 -- 78	Gifsy-2 prophage superoxide dismutase precursor (Cu-Zn)	stm1440 stm0924	_____________207__________245\n_____________\|____________\|\n5'-GAA...GCUUU____________CAGGG...CCA-3'\n______________GGUGGUCUCGCU\n______________\|\|\|:\|\|\|\|\|\|\|\|\n______________CCAUCAGAGCGA\n3'-UUU...UUUUC____________UGGCA...UCA-5'\n_____________\|____________\|\n_____________79___________42\n	78 -- 84	117 -- 123	-21.9622 kcal/mol	4.44224 kcal/mol	6.55795 kcal/mol	207 245@LB@ \| \|@LB@5'-GAA...GCUUU CAGGG...CCA-3'@LB@ GGUGGUCUCGCU@LB@ \|\|\|:\|\|\|\|\|\|\|\|@LB@ CCAUCAGAGCGA@LB@3'-UUU...UUUUC UGGCA...UCA-5'@LB@ \| \|@LB@ 79 42@LB@@LB@@LB@Energy -14.39 kcal/mol@LB@Hybridization Energy -21.9622 kcal/mol@LB@Unfolding Energy - mRNA 4.44224 kcal/mol@LB@Unfolding Energy - sRNA 6.55795 kcal/mol@LB@@LB@Position - mRNA 208 -- 244@LB@Position - sRNA 43 -- 78@LB@Position Seed - mRNA 78 -- 84@LB@Position Seed - sRNA 117 -- 123@LB@
180	0.009911	0.1961	stm0199	stfF	-15.44	0.100302	89 -- 133	44 -- 87	fimbrial protein		_____________88________________134\n_____________\|_________________\|\n5'-ACC...AUUUC___________G_____GGUCC...AUU-3'\n______________AAUACAGCGGC_GCAGC\n______________\|\|:\|\|\|:\|::\|_:\|\|:\|\n______________UUGUGUUGUUG_UGUUG\n3'-UUU...AACGU_________________UAGUG...UCA-5'\n_____________\|_________________\|\n_____________88________________43\n	93 -- 99	77 -- 83	-16.9774 kcal/mol	5.80505 kcal/mol	3.59664 kcal/mol	88 134@LB@ \| \|@LB@5'-ACC...AUUUC G GGUCC...AUU-3'@LB@ AAUACAGCGGC GCAGC@LB@ \|\|:\|\|\|:\|::\| :\|\|:\|@LB@ UUGUGUUGUUG UGUUG@LB@3'-UUU...AACGU UAGUG...UCA-5'@LB@ \| \|@LB@ 88 43@LB@@LB@@LB@Energy -15.44 kcal/mol@LB@Hybridization Energy -16.9774 kcal/mol@LB@Unfolding Energy - mRNA 5.80505 kcal/mol@LB@Unfolding Energy - sRNA 3.59664 kcal/mol@LB@@LB@Position - mRNA 89 -- 133@LB@Position - sRNA 44 -- 87@LB@Position Seed - mRNA 93 -- 99@LB@Position Seed - sRNA 77 -- 83@LB@
64	0.003108	0.1596	stm4162	thiF	-13.53	0.200092	247 -- 294	34 -- 76	molybdopterin/thiamine biosynthesis adenylyltransferase		_____________246___________________295\n_____________\|_____________________\|\n5'-GCA...GCUCG_______________A_____AGCAA...UUG-3'\n______________GCGAUAUCGCGAUUG_AGGCC\n______________:\|:\|:\|\|\|:\|:\|::\|_\|:\|\|\|\n______________UGUUGUAGUGUUGGC_UUCGG\n3'-UUU...UGUUG_______________A_____UUUUC...UCA-5'\n_____________\|_____________________\|\n_____________77____________________33\n	248 -- 254	69 -- 75	-25.2172 kcal/mol	7.66984 kcal/mol	8.92374 kcal/mol	246 295@LB@ \| \|@LB@5'-GCA...GCUCG A AGCAA...UUG-3'@LB@ GCGAUAUCGCGAUUG AGGCC@LB@ :\|:\|:\|\|\|:\|:\|::\| \|:\|\|\|@LB@ UGUUGUAGUGUUGGC UUCGG@LB@3'-UUU...UGUUG A UUUUC...UCA-5'@LB@ \| \|@LB@ 77 33@LB@@LB@@LB@Energy -13.53 kcal/mol@LB@Hybridization Energy -25.2172 kcal/mol@LB@Unfolding Energy - mRNA 7.66984 kcal/mol@LB@Unfolding Energy - sRNA 8.92374 kcal/mol@LB@@LB@Position - mRNA 247 -- 294@LB@Position - sRNA 34 -- 76@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 69 -- 75@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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