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: https://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
121	0.006021	0.1758	stm3903	ilvE	-13.34	0.214101	130 -- 170	39 -- 78	branched chain amino acid aminotransferase	_____________129__________________171\n_____________\|____________________\|\n5'-GGU...CCAGA___CU___C___U_______AAUCC...GUA-3'\n______________GCG___GC_ACA_CACAACA\n______________\|\|:___:\|_\|\|\|_\|\|\|\|\|\|\|\n______________CGU___UG_UGU_GUGUUGU\n3'-UUU...GUUAA___UUG__U___U_______AGUGU...UCA-5'\n_____________\|____________________\|\n_____________79___________________38\n	164 -- 170	71 -- 77	-14.4922 kcal/mol	2.12049 kcal/mol	3.80671 kcal/mol	129 171@LB@ \| \|@LB@5'-GGU...CCAGA CU C U AAUCC...GUA-3'@LB@ GCG GC ACA CACAACA@LB@ \|\|: :\| \|\|\| \|\|\|\|\|\|\|@LB@ CGU UG UGU GUGUUGU@LB@3'-UUU...GUUAA UUG U U AGUGU...UCA-5'@LB@ \| \|@LB@ 79 38@LB@@LB@@LB@Energy -13.34 kcal/mol@LB@Hybridization Energy -14.4922 kcal/mol@LB@Unfolding Energy - mRNA 2.12049 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 130 -- 170@LB@Position - sRNA 39 -- 78@LB@Position Seed - mRNA 164 -- 170@LB@Position Seed - sRNA 71 -- 77@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@
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@
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@
18	0.0003131	0.06194	stm0112	leuB	-16.29	0.072835	153 -- 217	44 -- 93	3-isopropylmalate dehydrogenase	_____________152___________218\n_____________\|_____________\|\n5'-AAA...AAAGA_____________AGCUC...GUU-3'\n______________AUUGC_AACGCAA\n______________\|\|\|\|\|_\|\|\|:\|\|\|\n______________UAACG_UUGUGUU\n3'-UUU...CUGGU_____U_______GUUGU...UCA-5'\n_____________\|_____________\|\n_____________94____________43\n	158 -- 164	81 -- 87	-11.6192 kcal/mol	1.90811 kcal/mol	3.57619 kcal/mol	152 218@LB@ \| \|@LB@5'-AAA...AAAGA AGCUC...GUU-3'@LB@ AUUGC AACGCAA@LB@ \|\|\|\|\| \|\|\|:\|\|\|@LB@ UAACG UUGUGUU@LB@3'-UUU...CUGGU U GUUGU...UCA-5'@LB@ \| \|@LB@ 94 43@LB@@LB@@LB@Energy -16.29 kcal/mol@LB@Hybridization Energy -11.6192 kcal/mol@LB@Unfolding Energy - mRNA 1.90811 kcal/mol@LB@Unfolding Energy - sRNA 3.57619 kcal/mol@LB@@LB@Position - mRNA 153 -- 217@LB@Position - sRNA 44 -- 93@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 81 -- 87@LB@
63	0.003024	0.1596	stm3563	livH	-16.49	0.067433	27 -- 175	36 -- 184	branched-chain amino acid ABC transporter permease LivH	_____________26_____________176\n_____________\|______________\|\n5'-GAU...GAAAU______________CGAUC...ACG-3'\n______________GGGA_UGAAAAAGG\n______________\|\|:\|_\|\|\|\|\|\|\|\|\|\n______________CCUU_ACUUUUUCC\n3'-UUU...CAUGU____C_________CAUCA...UCA-5'\n_____________\|______________\|\n_____________185____________35\n	65 -- 71	128 -- 134	-14.2251 kcal/mol	3.55711 kcal/mol	3.77758 kcal/mol	26 176@LB@ \| \|@LB@5'-GAU...GAAAU CGAUC...ACG-3'@LB@ GGGA UGAAAAAGG@LB@ \|\|:\| \|\|\|\|\|\|\|\|\|@LB@ CCUU ACUUUUUCC@LB@3'-UUU...CAUGU C CAUCA...UCA-5'@LB@ \| \|@LB@ 185 35@LB@@LB@@LB@Energy -16.49 kcal/mol@LB@Hybridization Energy -14.2251 kcal/mol@LB@Unfolding Energy - mRNA 3.55711 kcal/mol@LB@Unfolding Energy - sRNA 3.77758 kcal/mol@LB@@LB@Position - mRNA 27 -- 175@LB@Position - sRNA 36 -- 184@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 128 -- 134@LB@
61	0.002902	0.1596	stm3567	livJ	-18.03	0.037474	150 -- 196	40 -- 87	high-affinity branched-chain amino acid transporter	_____________149_______________________197\n_____________\|_________________________\|\n5'-CGG...ACAAU_____C____________A______AGAAU...CCG-3'\n______________AACAC_ACAACACA_CGU_ACAACC\n______________\|\|\|\|\|_\|\|\|\|\|\|\|\|_\|:\|_\|\|\|\|\|\|\n______________UUGUG_UGUUGUGU_GUA_UGUUGG\n3'-UUU...AACGU_____U________U___G______CAUUC...UCA-5'\n_____________\|_________________________\|\n_____________88________________________39\n	157 -- 163	74 -- 80	-27.1738 kcal/mol	3.63117 kcal/mol	8.28637 kcal/mol	149 197@LB@ \| \|@LB@5'-CGG...ACAAU C A AGAAU...CCG-3'@LB@ AACAC ACAACACA CGU ACAACC@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\| \|:\| \|\|\|\|\|\|@LB@ UUGUG UGUUGUGU GUA UGUUGG@LB@3'-UUU...AACGU U U G CAUUC...UCA-5'@LB@ \| \|@LB@ 88 39@LB@@LB@@LB@Energy -18.03 kcal/mol@LB@Hybridization Energy -27.1738 kcal/mol@LB@Unfolding Energy - mRNA 3.63117 kcal/mol@LB@Unfolding Energy - sRNA 8.28637 kcal/mol@LB@@LB@Position - mRNA 150 -- 196@LB@Position - sRNA 40 -- 87@LB@Position Seed - mRNA 157 -- 163@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@
11	0.0001804	0.05681	stm0959	lrp	-12.80	0.257711	163 -- 181	139 -- 159	leucine-responsive transcriptional regulator	_____________162_______________________________________________182\n_____________\|_________________________________________________\|\n5'-UGA...AGAGU________A_____GA________UAC______ACAAUAAUAAU_____AUAGC...AGC-3'\n______________CAGGCAGG_GUAGG_____AGGAA___AGAGAG___________GGUAG\n______________\|\|\|:\|\|\|\|_\|\|\|::_____\|\|\|\|\|___\|:\|:\|\|___________\|\|\|\|\|\n______________GUCUGUCC_CAUUU_____UCCUU___UUUUUC___________CCAUC\n3'-UUU...UACCU______________ACAUG_____CAC______________________AGAGC...UCA-5'\n_____________\|_________________________________________________\|\n_____________160_______________________________________________138\n	163 -- 169	153 -- 159	-28.6161 kcal/mol	5.81197 kcal/mol	10.0349 kcal/mol	162 182@LB@ \| \|@LB@5'-UGA...AGAGU A GA UAC ACAAUAAUAAU AUAGC...AGC-3'@LB@ CAGGCAGG GUAGG AGGAA AGAGAG GGUAG@LB@ \|\|\|:\|\|\|\| \|\|\|:: \|\|\|\|\| \|:\|:\|\| \|\|\|\|\|@LB@ GUCUGUCC CAUUU UCCUU UUUUUC CCAUC@LB@3'-UUU...UACCU ACAUG CAC AGAGC...UCA-5'@LB@ \| \|@LB@ 160 138@LB@@LB@@LB@Energy -12.80 kcal/mol@LB@Hybridization Energy -28.6161 kcal/mol@LB@Unfolding Energy - mRNA 5.81197 kcal/mol@LB@Unfolding Energy - sRNA 10.0349 kcal/mol@LB@@LB@Position - mRNA 163 -- 181@LB@Position - sRNA 139 -- 159@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 153 -- 159@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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