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
198	0.01098	0.197	stm2803	N/A	-14.51	0.140962	192 -- 262	36 -- 101	DNA-binding transcriptional regulator	_____________191___________________________263\n_____________\|_____________________________\|\n5'-GCU...AAAAA________UA___C_____UAU_______UCGCU...CGC-3'\n______________GCAGACCA__UGC__GCGC___CAGCACA\n______________\|\|\|\|\|\|\|\|__\|\|\|__:\|:\|___\|\|:\|\|\|\|\n______________CGUCUGGU__ACG__UGUG___GUUGUGU\n3'-UUU...CUUAG________UA___UU____UU________UGUAG...UCA-5'\n_____________\|_____________________________\|\n_____________102___________________________35\n	213 -- 219	74 -- 80	-31.0005 kcal/mol	8.41541 kcal/mol	13.1066 kcal/mol	191 263@LB@ \| \|@LB@5'-GCU...AAAAA UA C UAU UCGCU...CGC-3'@LB@ GCAGACCA UGC GCGC CAGCACA@LB@ \|\|\|\|\|\|\|\| \|\|\| :\|:\| \|\|:\|\|\|\|@LB@ CGUCUGGU ACG UGUG GUUGUGU@LB@3'-UUU...CUUAG UA UU UU UGUAG...UCA-5'@LB@ \| \|@LB@ 102 35@LB@@LB@@LB@Energy -14.51 kcal/mol@LB@Hybridization Energy -31.0005 kcal/mol@LB@Unfolding Energy - mRNA 8.41541 kcal/mol@LB@Unfolding Energy - sRNA 13.1066 kcal/mol@LB@@LB@Position - mRNA 192 -- 262@LB@Position - sRNA 36 -- 101@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 74 -- 80@LB@
4	5.758e-05	0.04123	stm3564	livK	-17.90	0.039430	157 -- 215	37 -- 90	leucine ABC transporter subunit substrate-binding protein LivK	_____________156______________________216\n_____________\|________________________\|\n5'-UUU...GCAAA_____A__________________AUGGG...CGA-3'\n______________AAACA_AAC_AUAUAACAUCACGA\n______________\|\|\|\|\|_\|\|\|_\|:\|:\|\|\|\|\|\|\|\|:\|\n______________UUUGU_UUG_UGUGUUGUAGUGUU\n3'-UUU...UAACG_____G___U______________GGCAU...UCA-5'\n_____________\|________________________\|\n_____________91_______________________36\n	178 -- 184	65 -- 71	-21.8749 kcal/mol	0.694231 kcal/mol	6.38817 kcal/mol	156 216@LB@ \| \|@LB@5'-UUU...GCAAA A AUGGG...CGA-3'@LB@ AAACA AAC AUAUAACAUCACGA@LB@ \|\|\|\|\| \|\|\| \|:\|:\|\|\|\|\|\|\|\|:\|@LB@ UUUGU UUG UGUGUUGUAGUGUU@LB@3'-UUU...UAACG G U GGCAU...UCA-5'@LB@ \| \|@LB@ 91 36@LB@@LB@@LB@Energy -17.90 kcal/mol@LB@Hybridization Energy -21.8749 kcal/mol@LB@Unfolding Energy - mRNA 0.694231 kcal/mol@LB@Unfolding Energy - sRNA 6.38817 kcal/mol@LB@@LB@Position - mRNA 157 -- 215@LB@Position - sRNA 37 -- 90@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 65 -- 71@LB@
14	0.0002233	0.05681	stm3843	trmE	-16.53	0.066478	207 -- 249	37 -- 85	tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE	_____________206______________250\n_____________\|________________\|\n5'-UGA...CAUGA________________UAUCG...CGC-3'\n______________GC___CAUAACGACAC\n______________\|\|___\|\|:\|\|\|:\|\|\|\|\n______________CG___GUGUUGUUGUG\n3'-UUU...GUUAA__UUU___________UUGUA...UCA-5'\n_____________\|________________\|\n_____________86_______________36\n	211 -- 217	75 -- 81	-15.3625 kcal/mol	2.22645 kcal/mol	3.72363 kcal/mol	206 250@LB@ \| \|@LB@5'-UGA...CAUGA UAUCG...CGC-3'@LB@ GC CAUAACGACAC@LB@ \|\| \|\|:\|\|\|:\|\|\|\|@LB@ CG GUGUUGUUGUG@LB@3'-UUU...GUUAA UUU UUGUA...UCA-5'@LB@ \| \|@LB@ 86 36@LB@@LB@@LB@Energy -16.53 kcal/mol@LB@Hybridization Energy -15.3625 kcal/mol@LB@Unfolding Energy - mRNA 2.22645 kcal/mol@LB@Unfolding Energy - sRNA 3.72363 kcal/mol@LB@@LB@Position - mRNA 207 -- 249@LB@Position - sRNA 37 -- 85@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 75 -- 81@LB@
29	0.0007392	0.08814	stm3096	yqgE	-16.45	0.068552	198 -- 251	37 -- 84	DUF179 domain-containing protein	_____________197___________252\n_____________\|_____________\|\n5'-UGG...UAUAU_____________CAGGA...GCG-3'\n______________UUGCGAGCACAAC\n______________\|\|\|\|:\|:\|\|\|\|\|\|\n______________AACGUUUGUGUUG\n3'-UUU...UGGUU_____________UUGUG...UCA-5'\n_____________\|_____________\|\n_____________85____________36\n	284 -- 290	80 -- 86	-18.5161 kcal/mol	2.82597 kcal/mol	3.5889 kcal/mol	197 252@LB@ \| \|@LB@5'-UGG...UAUAU CAGGA...GCG-3'@LB@ UUGCGAGCACAAC@LB@ \|\|\|\|:\|:\|\|\|\|\|\|@LB@ AACGUUUGUGUUG@LB@3'-UUU...UGGUU UUGUG...UCA-5'@LB@ \| \|@LB@ 85 36@LB@@LB@@LB@Energy -16.45 kcal/mol@LB@Hybridization Energy -18.5161 kcal/mol@LB@Unfolding Energy - mRNA 2.82597 kcal/mol@LB@Unfolding Energy - sRNA 3.5889 kcal/mol@LB@@LB@Position - mRNA 198 -- 251@LB@Position - sRNA 37 -- 84@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 80 -- 86@LB@
36	0.00125	0.1215	stm3523	glpR	-16.55	0.065942	207 -- 266	37 -- 89	DeoR/GlpR family transcriptional regulator	_____________206________________267\n_____________\|__________________\|\n5'-UUG...UGAAA__________________GCGAU...CGC-3'\n______________CAAACACAACGGCAUGAC\n______________\|\|\|\|\|\|\|\|\|\|::\|\|::\|\|\n______________GUUUGUGUUGUUGUGUUG\n3'-UUU...UUAAC__________________UAGUG...UCA-5'\n_____________\|__________________\|\n_____________90_________________36\n	218 -- 224	72 -- 78	-24.6143 kcal/mol	5.8046 kcal/mol	3.79561 kcal/mol	206 267@LB@ \| \|@LB@5'-UUG...UGAAA GCGAU...CGC-3'@LB@ CAAACACAACGGCAUGAC@LB@ \|\|\|\|\|\|\|\|\|\|::\|\|::\|\|@LB@ GUUUGUGUUGUUGUGUUG@LB@3'-UUU...UUAAC UAGUG...UCA-5'@LB@ \| \|@LB@ 90 36@LB@@LB@@LB@Energy -16.55 kcal/mol@LB@Hybridization Energy -24.6143 kcal/mol@LB@Unfolding Energy - mRNA 5.8046 kcal/mol@LB@Unfolding Energy - sRNA 3.79561 kcal/mol@LB@@LB@Position - mRNA 207 -- 266@LB@Position - sRNA 37 -- 89@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 72 -- 78@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@
43	0.001574	0.1267	stm4453	treC	-17.28	0.050040	221 -- 269	37 -- 81	trehalose- 6-P hydrolase	_____________220____________________270\n_____________\|______________________\|\n5'-CGU...CGCAC_______AA_____________UAUUC...GCG-3'\n______________UUGCAGG__ACAACAAU__GAC\n______________\|\|\|\|\|::__\|\|\|\|\|\|\|:__:\|\|\n______________AACGUUU__UGUUGUUG__UUG\n3'-UUU...UGGUU_______G_________UG___UAGUG...UCA-5'\n_____________\|______________________\|\n_____________82_____________________36\n	196 -- 202	77 -- 83	-15.8671 kcal/mol	3.0955 kcal/mol	3.80821 kcal/mol	220 270@LB@ \| \|@LB@5'-CGU...CGCAC AA UAUUC...GCG-3'@LB@ UUGCAGG ACAACAAU GAC@LB@ \|\|\|\|\|:: \|\|\|\|\|\|\|: :\|\|@LB@ AACGUUU UGUUGUUG UUG@LB@3'-UUU...UGGUU G UG UAGUG...UCA-5'@LB@ \| \|@LB@ 82 36@LB@@LB@@LB@Energy -17.28 kcal/mol@LB@Hybridization Energy -15.8671 kcal/mol@LB@Unfolding Energy - mRNA 3.0955 kcal/mol@LB@Unfolding Energy - sRNA 3.80821 kcal/mol@LB@@LB@Position - mRNA 221 -- 269@LB@Position - sRNA 37 -- 81@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 77 -- 83@LB@
47	0.001676	0.127	stm0637	dacA	-17.91	0.039191	14 -- 64	37 -- 92	serine-type D-Ala-D-Ala carboxypeptidase	_____________13____________________65\n_____________\|_____________________\|\n5'-GUU...AACGU_________GA__________UACAG...AUA-3'\n______________UUGCAAACA____AGCACAAU\n______________\|\|\|\|\|\|\|\|\|____\|:\|\|\|\|\|:\n______________AACGUUUGU____UUGUGUUG\n3'-UUU...UGGUU_________GUUG________UAGUG...UCA-5'\n_____________\|_____________________\|\n_____________93____________________36\n	26 -- 32	72 -- 78	-19.7119 kcal/mol	3.03223 kcal/mol	3.80821 kcal/mol	13 65@LB@ \| \|@LB@5'-GUU...AACGU GA UACAG...AUA-3'@LB@ UUGCAAACA AGCACAAU@LB@ \|\|\|\|\|\|\|\|\| \|:\|\|\|\|\|:@LB@ AACGUUUGU UUGUGUUG@LB@3'-UUU...UGGUU GUUG UAGUG...UCA-5'@LB@ \| \|@LB@ 93 36@LB@@LB@@LB@Energy -17.91 kcal/mol@LB@Hybridization Energy -19.7119 kcal/mol@LB@Unfolding Energy - mRNA 3.03223 kcal/mol@LB@Unfolding Energy - sRNA 3.80821 kcal/mol@LB@@LB@Position - mRNA 14 -- 64@LB@Position - sRNA 37 -- 92@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 72 -- 78@LB@
85	0.003998	0.1596	stm1098	hpaC	-22.15	0.007534	132 -- 187	37 -- 90	4-hydroxyphenylacetate 3-monooxygenase reductase component	_____________131________________________________________188\n_____________\|__________________________________________\|\n5'-UAC...GUUUC___UUU__________G_________AU______GA______GCUGA...GCG-3'\n______________GCA___GCACAAUAAC_ACGACAUCA__CAACUG__UAAGCU\n______________\|\|\|___:\|\|\|\|\|:\|\|\|_\|\|:\|\|\|\|\|\|__\|\|\|\|:\|__\|\|\|\|\|:\n______________CGU___UGUGUUGUUG_UGUUGUAGU__GUUGGC__AUUCGG\n3'-UUU...GUUAA___U______________________________________UUUUC...UCA-5'\n_____________\|__________________________________________\|\n_____________91_________________________________________36\n	151 -- 157	68 -- 74	-38.4357 kcal/mol	7.30976 kcal/mol	11.8287 kcal/mol	131 188@LB@ \| \|@LB@5'-UAC...GUUUC UUU G AU GA GCUGA...GCG-3'@LB@ GCA GCACAAUAAC ACGACAUCA CAACUG UAAGCU@LB@ \|\|\| :\|\|\|\|\|:\|\|\| \|\|:\|\|\|\|\|\| \|\|\|\|:\| \|\|\|\|\|:@LB@ CGU UGUGUUGUUG UGUUGUAGU GUUGGC AUUCGG@LB@3'-UUU...GUUAA U UUUUC...UCA-5'@LB@ \| \|@LB@ 91 36@LB@@LB@@LB@Energy -22.15 kcal/mol@LB@Hybridization Energy -38.4357 kcal/mol@LB@Unfolding Energy - mRNA 7.30976 kcal/mol@LB@Unfolding Energy - sRNA 11.8287 kcal/mol@LB@@LB@Position - mRNA 132 -- 187@LB@Position - sRNA 37 -- 90@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 68 -- 74@LB@
101	0.005112	0.1728	stm0113	leuA	-13.72	0.187230	187 -- 230	37 -- 84	2-isopropylmalate synthase	_____________186_____________________231\n_____________\|_______________________\|\n5'-AUA...UGGAG____G_____________G____AGCAA...UGG-3'\n______________ACAA_GAC_C_ACAUCAU_AGCC\n______________\|\|\|\|_:\|\|_\|_\|\|\|\|\|\|:_\|:\|\|\n______________UGUU_UUG_G_UGUAGUG_UUGG\n3'-UUU...GUUUG____G___U_U____________CAUUC...UCA-5'\n_____________\|_______________________\|\n_____________85______________________36\n	196 -- 202	67 -- 73	-19.8594 kcal/mol	2.76514 kcal/mol	8.15907 kcal/mol	186 231@LB@ \| \|@LB@5'-AUA...UGGAG G G AGCAA...UGG-3'@LB@ ACAA GAC C ACAUCAU AGCC@LB@ \|\|\|\| :\|\| \| \|\|\|\|\|\|: \|:\|\|@LB@ UGUU UUG G UGUAGUG UUGG@LB@3'-UUU...GUUUG G U U CAUUC...UCA-5'@LB@ \| \|@LB@ 85 36@LB@@LB@@LB@Energy -13.72 kcal/mol@LB@Hybridization Energy -19.8594 kcal/mol@LB@Unfolding Energy - mRNA 2.76514 kcal/mol@LB@Unfolding Energy - sRNA 8.15907 kcal/mol@LB@@LB@Position - mRNA 187 -- 230@LB@Position - sRNA 37 -- 84@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 67 -- 73@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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