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
42	0.001433	0.1215	stm1318	katE	-13.62	0.194137	191 -- 230	43 -- 82	catalase HPII		_____________190_________231\n_____________\|___________\|\n5'-GGC...UCUGC___________UCCCC...AUC-3'\n______________CGUUCCG_CUC\n______________\|\|\|\|\|\|\|_\|\|\|\n______________GCAAGGC_GAG\n3'-UUU...GAAAA_______C___UCCUUCA-5'\n_____________\|___________\|\n_____________83__________42\n	99 -- 105	12 -- 18	-14.968 kcal/mol	1.4568 kcal/mol	6.53351 kcal/mol	190 231@LB@ \| \|@LB@5'-GGC...UCUGC UCCCC...AUC-3'@LB@ CGUUCCG CUC@LB@ \|\|\|\|\|\|\| \|\|\|@LB@ GCAAGGC GAG@LB@3'-UUU...GAAAA C UCCUUCA-5'@LB@ \| \|@LB@ 83 42@LB@@LB@@LB@Energy -13.62 kcal/mol@LB@Hybridization Energy -14.968 kcal/mol@LB@Unfolding Energy - mRNA 1.4568 kcal/mol@LB@Unfolding Energy - sRNA 6.53351 kcal/mol@LB@@LB@Position - mRNA 191 -- 230@LB@Position - sRNA 43 -- 82@LB@Position Seed - mRNA 99 -- 105@LB@Position Seed - sRNA 12 -- 18@LB@
44	0.001631	0.1267	stm1318	katE	-13.62	0.194137	191 -- 230	43 -- 82	catalase HPII		_____________190_________231\n_____________\|___________\|\n5'-GGC...UCUGC___________UCCCC...AUC-3'\n______________CGUUCCG_CUC\n______________\|\|\|\|\|\|\|_\|\|\|\n______________GCAAGGC_GAG\n3'-UUU...GAAAA_______C___UCCUUCA-5'\n_____________\|___________\|\n_____________83__________42\n	99 -- 105	12 -- 18	-14.968 kcal/mol	1.4568 kcal/mol	6.53351 kcal/mol	190 231@LB@ \| \|@LB@5'-GGC...UCUGC UCCCC...AUC-3'@LB@ CGUUCCG CUC@LB@ \|\|\|\|\|\|\| \|\|\|@LB@ GCAAGGC GAG@LB@3'-UUU...GAAAA C UCCUUCA-5'@LB@ \| \|@LB@ 83 42@LB@@LB@@LB@Energy -13.62 kcal/mol@LB@Hybridization Energy -14.968 kcal/mol@LB@Unfolding Energy - mRNA 1.4568 kcal/mol@LB@Unfolding Energy - sRNA 6.53351 kcal/mol@LB@@LB@Position - mRNA 191 -- 230@LB@Position - sRNA 43 -- 82@LB@Position Seed - mRNA 99 -- 105@LB@Position Seed - sRNA 12 -- 18@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@
197	0.01093	0.197	stm2924	rpoS	-16.80	0.060020	191 -- 216	36 -- 60	RNA polymerase sigma factor RpoS		_____________190________________________________217\n_____________\|__________________________________\|\n___5'-CGGGAACA_________U____C___GCAAAAAA________AUGGG...AGG-3'\n______________ACAGGAAGU_AAGG_GGG________UCGCUACU\n______________\|\|\|\|\|\|\|\|\|_\|\|::_\|\|\|________\|\|\|\|\|\|\|:\n______________UGUCCUUCA_UUUU_CCC________AGCGAUGG\n3'-UUU...UUACA_________C____U___AUCAG___________CACCA...UCA-5'\n_____________\|__________________________________\|\n_____________61_________________________________35\n	36 -- 42	114 -- 120	-31.3768 kcal/mol	8.74888 kcal/mol	8.99738 kcal/mol	190 217@LB@ \| \|@LB@ 5'-CGGGAACA U C GCAAAAAA AUGGG...AGG-3'@LB@ ACAGGAAGU AAGG GGG UCGCUACU@LB@ \|\|\|\|\|\|\|\|\| \|\|:: \|\|\| \|\|\|\|\|\|\|:@LB@ UGUCCUUCA UUUU CCC AGCGAUGG@LB@3'-UUU...UUACA C U AUCAG CACCA...UCA-5'@LB@ \| \|@LB@ 61 35@LB@@LB@@LB@Energy -16.80 kcal/mol@LB@Hybridization Energy -31.3768 kcal/mol@LB@Unfolding Energy - mRNA 8.74888 kcal/mol@LB@Unfolding Energy - sRNA 8.99738 kcal/mol@LB@@LB@Position - mRNA 191 -- 216@LB@Position - sRNA 36 -- 60@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 114 -- 120@LB@
147	0.007823	0.1845	stm3477	cysG	-15.08	0.114738	192 -- 245	61 -- 111	uroporphyrinogen-III C-methyltransferase		_____________191____________________________________________246\n_____________\|______________________________________________\|\n5'-UCC...UAAGG___AAU____________U____CU___UUUUGU____U_______CGCGA...AAG-3'\n______________GGU____GUCGUGGACCA_UUGC__AUA______CAAU_ACGCGAC\n______________\|\|\|____:\|\|\|::\|\|\|\|\|_\|\|\|\|__\|:\|______\|\|\|:_\|\|:\|:\|\|\n______________CCA____UAGCGUCUGGU_AACG__UGU______GUUG_UGUGUUG\n3'-UUU...UGGCA___GACU___________U____UU_____________U_______UAGUG...UCA-5'\n_____________\|______________________________________________\|\n_____________112____________________________________________60\n	230 -- 236	72 -- 78	-36.0085 kcal/mol	10.6439 kcal/mol	13.6111 kcal/mol	191 246@LB@ \| \|@LB@5'-UCC...UAAGG AAU U CU UUUUGU U CGCGA...AAG-3'@LB@ GGU GUCGUGGACCA UUGC AUA CAAU ACGCGAC@LB@ \|\|\| :\|\|\|::\|\|\|\|\| \|\|\|\| \|:\| \|\|\|: \|\|:\|:\|\|@LB@ CCA UAGCGUCUGGU AACG UGU GUUG UGUGUUG@LB@3'-UUU...UGGCA GACU U UU U UAGUG...UCA-5'@LB@ \| \|@LB@ 112 60@LB@@LB@@LB@Energy -15.08 kcal/mol@LB@Hybridization Energy -36.0085 kcal/mol@LB@Unfolding Energy - mRNA 10.6439 kcal/mol@LB@Unfolding Energy - sRNA 13.6111 kcal/mol@LB@@LB@Position - mRNA 192 -- 245@LB@Position - sRNA 61 -- 111@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 72 -- 78@LB@
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@
41	0.001426	0.1215	stm3718	rfaI	-15.09	0.114319	193 -- 209	157 -- 173	lipopolysaccharide 1 3-galactosyltransferase	stm3717	_____________192_______________210\n_____________\|_________________\|\n5'-AUG...AAAAG___________A_____AAAUA...GGA-3'\n______________UGAUCACUAUG_GCAGA\n______________\|:\|\|\|\|\|\|\|\|\|_:\|\|\|\|\n______________AUUAGUGAUAC_UGUCU\n3'-UUU...AUGUA___________C_____GUCCC...UCA-5'\n_____________\|_________________\|\n_____________174_______________156\n	197 -- 203	163 -- 169	-20.9664 kcal/mol	2.81615 kcal/mol	3.98136 kcal/mol	192 210@LB@ \| \|@LB@5'-AUG...AAAAG A AAAUA...GGA-3'@LB@ UGAUCACUAUG GCAGA@LB@ \|:\|\|\|\|\|\|\|\|\| :\|\|\|\|@LB@ AUUAGUGAUAC UGUCU@LB@3'-UUU...AUGUA C GUCCC...UCA-5'@LB@ \| \|@LB@ 174 156@LB@@LB@@LB@Energy -15.09 kcal/mol@LB@Hybridization Energy -20.9664 kcal/mol@LB@Unfolding Energy - mRNA 2.81615 kcal/mol@LB@Unfolding Energy - sRNA 3.98136 kcal/mol@LB@@LB@Position - mRNA 193 -- 209@LB@Position - sRNA 157 -- 173@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 163 -- 169@LB@
161	0.008343	0.1845	stm3321	yhbH	-14.15	0.160801	194 -- 246	48 -- 88	ribosomal subunit interface protein		_____________193______________________247\n_____________\|________________________\|\n5'-GAU...AAGGA______UAU_____U_________CGGAC...GGA-3'\n______________AGACAC___GCAGC_CAAUAUCAC\n______________\|:\|\|\|\|___:\|\|:\|_\|\|\|:\|\|\|\|\|\n______________UUUGUG___UGUUG_GUUGUAGUG\n3'-UUU...UAACG______U_______U_________UUGGC...UCA-5'\n_____________\|________________________\|\n_____________89_______________________47\n	211 -- 217	67 -- 73	-22.4132 kcal/mol	2.65406 kcal/mol	5.48747 kcal/mol	193 247@LB@ \| \|@LB@5'-GAU...AAGGA UAU U CGGAC...GGA-3'@LB@ AGACAC GCAGC CAAUAUCAC@LB@ \|:\|\|\|\| :\|\|:\| \|\|\|:\|\|\|\|\|@LB@ UUUGUG UGUUG GUUGUAGUG@LB@3'-UUU...UAACG U U UUGGC...UCA-5'@LB@ \| \|@LB@ 89 47@LB@@LB@@LB@Energy -14.15 kcal/mol@LB@Hybridization Energy -22.4132 kcal/mol@LB@Unfolding Energy - mRNA 2.65406 kcal/mol@LB@Unfolding Energy - sRNA 5.48747 kcal/mol@LB@@LB@Position - mRNA 194 -- 246@LB@Position - sRNA 48 -- 88@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 67 -- 73@LB@
187	0.01045	0.1967	stm4558	rimI	-18.19	0.035171	194 -- 252	42 -- 91	ribosomal-protein-alanine N-acetyltransferase		_____________193______________________________________253\n_____________\|________________________________________\|\n5'-GAC...AAAUC_________G__________UUCUAUCCUCAG________AUCUC...UCG-3'\n______________UGCGAACAU___AACACGAU____________CACGACCG\n______________\|\|\|:\|\|\|\|:___\|\|\|\|\|:\|:____________\|\|\|:\|\|\|\|\n______________ACGUUUGUG___UUGUGUUG____________GUGUUGGC\n3'-UUU...GGUUA_________UUG________UA__________________AUUCG...UCA-5'\n_____________\|________________________________________\|\n_____________92_______________________________________41\n	225 -- 231	62 -- 68	-28.9909 kcal/mol	5.96366 kcal/mol	8.62907 kcal/mol	193 253@LB@ \| \|@LB@5'-GAC...AAAUC G UUCUAUCCUCAG AUCUC...UCG-3'@LB@ UGCGAACAU AACACGAU CACGACCG@LB@ \|\|\|:\|\|\|\|: \|\|\|\|\|:\|: \|\|\|:\|\|\|\|@LB@ ACGUUUGUG UUGUGUUG GUGUUGGC@LB@3'-UUU...GGUUA UUG UA AUUCG...UCA-5'@LB@ \| \|@LB@ 92 41@LB@@LB@@LB@Energy -18.19 kcal/mol@LB@Hybridization Energy -28.9909 kcal/mol@LB@Unfolding Energy - mRNA 5.96366 kcal/mol@LB@Unfolding Energy - sRNA 8.62907 kcal/mol@LB@@LB@Position - mRNA 194 -- 252@LB@Position - sRNA 42 -- 91@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 62 -- 68@LB@
98	0.004857	0.1728	stm2811	proX	-15.53	0.097032	195 -- 224	56 -- 84	glycine betaine ABC transporter substrate-binding protein		_____________194________________________225\n_____________\|__________________________\|\n5'-GCA...AAGGA__________________________UAUUU...CUA-3'\n______________ACAACGAUGCGACAU____ACCGUGA\n______________\|\|\|\|\|:\|::\|:\|\|\|\|____\|\|\|\|\|:\|\n______________UGUUGUUGUGUUGUA____UGGCAUU\n3'-UUU...GUUUG_______________GUGU_______CGGUU...UCA-5'\n_____________\|__________________________\|\n_____________85_________________________55\n	210 -- 216	59 -- 65	-26.0076 kcal/mol	3.5169 kcal/mol	9.80321 kcal/mol	194 225@LB@ \| \|@LB@5'-GCA...AAGGA UAUUU...CUA-3'@LB@ ACAACGAUGCGACAU ACCGUGA@LB@ \|\|\|\|\|:\|::\|:\|\|\|\| \|\|\|\|\|:\|@LB@ UGUUGUUGUGUUGUA UGGCAUU@LB@3'-UUU...GUUUG GUGU CGGUU...UCA-5'@LB@ \| \|@LB@ 85 55@LB@@LB@@LB@Energy -15.53 kcal/mol@LB@Hybridization Energy -26.0076 kcal/mol@LB@Unfolding Energy - mRNA 3.5169 kcal/mol@LB@Unfolding Energy - sRNA 9.80321 kcal/mol@LB@@LB@Position - mRNA 195 -- 224@LB@Position - sRNA 56 -- 84@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 59 -- 65@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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