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
24	0.000609	0.08814	stm3510	yhgH	-18.34	0.033208	106 -- 153	42 -- 84	DNA utilization protein GntX		_____________105____________________________________154\n_____________\|______________________________________\|\n5'-CCG...UCCGU____________G__G___AUUUCCCUC__________UGCCA...GCG-3'\n______________GCAGCAGCACAA_AU_ACA_________GCCGUAGGUC\n______________:\|\|:\|\|:\|\|\|\|\|_\|\|_\|\|\|_________:\|\|\|\|\|:\|:\|\n______________UGUUGUUGUGUU_UA_UGU_________UGGCAUUCGG\n3'-UUU...GUUUG____________G__G______________________UUUUC...UCA-5'\n_____________\|______________________________________\|\n_____________85_____________________________________41\n	135 -- 141	58 -- 64	-35.7194 kcal/mol	10.0869 kcal/mol	11.5136 kcal/mol	105 154@LB@ \| \|@LB@5'-CCG...UCCGU G G AUUUCCCUC UGCCA...GCG-3'@LB@ GCAGCAGCACAA AU ACA GCCGUAGGUC@LB@ :\|\|:\|\|:\|\|\|\|\| \|\| \|\|\| :\|\|\|\|\|:\|:\|@LB@ UGUUGUUGUGUU UA UGU UGGCAUUCGG@LB@3'-UUU...GUUUG G G UUUUC...UCA-5'@LB@ \| \|@LB@ 85 41@LB@@LB@@LB@Energy -18.34 kcal/mol@LB@Hybridization Energy -35.7194 kcal/mol@LB@Unfolding Energy - mRNA 10.0869 kcal/mol@LB@Unfolding Energy - sRNA 11.5136 kcal/mol@LB@@LB@Position - mRNA 106 -- 153@LB@Position - sRNA 42 -- 84@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 58 -- 64@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@
153	0.008123	0.1845	stm2512	xseA	-14.57	0.138273	215 -- 252	42 -- 82	exodeoxyribonuclease VII large subunit		_____________214________253\n_____________\|__________\|\n5'-CGU...UUUUU__________GCCUU...GCG-3'\n______________ACCGUAAGCC\n______________\|\|\|\|\|\|\|\|\|\|\n______________UGGCAUUCGG\n3'-UUU...AGUGU__________UUUUC...UCA-5'\n_____________\|__________\|\n_____________83_________41\n	234 -- 240	56 -- 62	-17.1871 kcal/mol	1.1981 kcal/mol	7.48121 kcal/mol	214 253@LB@ \| \|@LB@5'-CGU...UUUUU GCCUU...GCG-3'@LB@ ACCGUAAGCC@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UGGCAUUCGG@LB@3'-UUU...AGUGU UUUUC...UCA-5'@LB@ \| \|@LB@ 83 41@LB@@LB@@LB@Energy -14.57 kcal/mol@LB@Hybridization Energy -17.1871 kcal/mol@LB@Unfolding Energy - mRNA 1.1981 kcal/mol@LB@Unfolding Energy - sRNA 7.48121 kcal/mol@LB@@LB@Position - mRNA 215 -- 252@LB@Position - sRNA 42 -- 82@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 56 -- 62@LB@
77	0.003608	0.1596	stm4473	yjgM	-11.12	0.437983	252 -- 285	42 -- 82	GNAT family N-acetyltransferase		_____________251________________286\n_____________\|__________________\|\n5'-AUU...CGCCG________CC___C____AUGCC...ACG-3'\n______________AAUCACUA___GC_GACA\n______________\|\|\|\|\|\|\|\|___:\|_\|\|\|\|\n______________UUAGUGAU___UG_CUGU\n3'-UUU...UGUAA________ACC__U____CCCAU...UCA-5'\n_____________\|__________________\|\n_____________83_________________41\n	240 -- 246	165 -- 171	-13.0222 kcal/mol	3.39479 kcal/mol	3.49149 kcal/mol	251 286@LB@ \| \|@LB@5'-AUU...CGCCG CC C AUGCC...ACG-3'@LB@ AAUCACUA GC GACA@LB@ \|\|\|\|\|\|\|\| :\| \|\|\|\|@LB@ UUAGUGAU UG CUGU@LB@3'-UUU...UGUAA ACC U CCCAU...UCA-5'@LB@ \| \|@LB@ 83 41@LB@@LB@@LB@Energy -11.12 kcal/mol@LB@Hybridization Energy -13.0222 kcal/mol@LB@Unfolding Energy - mRNA 3.39479 kcal/mol@LB@Unfolding Energy - sRNA 3.49149 kcal/mol@LB@@LB@Position - mRNA 252 -- 285@LB@Position - sRNA 42 -- 82@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 165 -- 171@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@
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@
111	0.005436	0.1728	stm2683	yfjB	-15.36	0.103307	255 -- 299	43 -- 90	NAD(+) kinase		_____________254___________________________________________________________________300\n_____________\|_____________________________________________________________________\|\n5'-CUC...UUCGC__________GAU____UU______UUCAA__________ACUCACAUU_____AUCAAUCU_______AAGGA...AGG-3'\n______________UUAUUAUGGG___CAGA__CAGGGU________GGGAAGU___________GUC________UCGCUAC\n______________\|:\|:\|\|\|\|\|:___\|\|\|\|__\|\|\|\|\|\|________:\|\|\|\|\|\|___________\|\|\|________\|\|\|\|\|\|\|\n______________AGUGAUACCU___GUCU__GUCCCA________UCCUUCA___________CAG________AGCGAUG\n3'-UUU...UAAUU_________________________UUUACAUG_______CUUUUUCCCAU__________________GCACC...UCA-5'\n_____________\|_____________________________________________________________________\|\n_____________91____________________________________________________________________42\n	179 -- 185	115 -- 121	-40.6869 kcal/mol	14.2494 kcal/mol	12.858 kcal/mol	254 300@LB@ \| \|@LB@5'-CUC...UUCGC GAU UU UUCAA ACUCACAUU AUCAAUCU AAGGA...AGG-3'@LB@ UUAUUAUGGG CAGA CAGGGU GGGAAGU GUC UCGCUAC@LB@ \|:\|:\|\|\|\|\|: \|\|\|\| \|\|\|\|\|\| :\|\|\|\|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ AGUGAUACCU GUCU GUCCCA UCCUUCA CAG AGCGAUG@LB@3'-UUU...UAAUU UUUACAUG CUUUUUCCCAU GCACC...UCA-5'@LB@ \| \|@LB@ 91 42@LB@@LB@@LB@Energy -15.36 kcal/mol@LB@Hybridization Energy -40.6869 kcal/mol@LB@Unfolding Energy - mRNA 14.2494 kcal/mol@LB@Unfolding Energy - sRNA 12.858 kcal/mol@LB@@LB@Position - mRNA 255 -- 299@LB@Position - sRNA 43 -- 90@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 115 -- 121@LB@
169	0.009276	0.1945	stm0495	ybaK	-13.73	0.186840	16 -- 30	44 -- 58	aminoacyl-tRNA deacylase		_____________15_________________31\n_____________\|__________________\|\n5'-AAA...CAUUC____CU__G_________CGAAU...UGG-3'\n______________ACAC__AC_AUCACGAUC\n______________\|\|\|\|__\|\|_\|\|\|\|\|:\|:\|\n______________UGUG__UG_UAGUGUUGG\n3'-UUU...GUUGU____U_____________CAUUC...UCA-5'\n_____________\|__________________\|\n_____________59_________________43\n	264 -- 270	63 -- 69	-14.6876 kcal/mol	0.727125 kcal/mol	6.44907 kcal/mol	15 31@LB@ \| \|@LB@5'-AAA...CAUUC CU G CGAAU...UGG-3'@LB@ ACAC AC AUCACGAUC@LB@ \|\|\|\| \|\| \|\|\|\|\|:\|:\|@LB@ UGUG UG UAGUGUUGG@LB@3'-UUU...GUUGU U CAUUC...UCA-5'@LB@ \| \|@LB@ 59 43@LB@@LB@@LB@Energy -13.73 kcal/mol@LB@Hybridization Energy -14.6876 kcal/mol@LB@Unfolding Energy - mRNA 0.727125 kcal/mol@LB@Unfolding Energy - sRNA 6.44907 kcal/mol@LB@@LB@Position - mRNA 16 -- 30@LB@Position - sRNA 44 -- 58@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 63 -- 69@LB@
160	0.008331	0.1845	stm0002	thrA	-15.10	0.113872	18 -- 81	44 -- 90	bifunctional aspartate kinase/homoserine dehydrogenase I		_____________17______________________82\n_____________\|_______________________\|\n5'-CCA...UACAA________AAUAA__________AGUAC...UAG-3'\n______________GACAGACA_____AAAUG_ACAG\n______________\|\|\|\|\|\|\|\|_____\|\|\|\|\|_\|\|\|\|\n______________CUGUCUGU_____UUUAC_UGUC\n3'-UUU...GAUAC________CCCA______A____CUUCA...UCA-5'\n_____________\|_______________________\|\n_____________91______________________43\n	19 -- 25	155 -- 161	-19.4516 kcal/mol	0.236149 kcal/mol	3.68511 kcal/mol	17 82@LB@ \| \|@LB@5'-CCA...UACAA AAUAA AGUAC...UAG-3'@LB@ GACAGACA AAAUG ACAG@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\| \|\|\|\|@LB@ CUGUCUGU UUUAC UGUC@LB@3'-UUU...GAUAC CCCA A CUUCA...UCA-5'@LB@ \| \|@LB@ 91 43@LB@@LB@@LB@Energy -15.10 kcal/mol@LB@Hybridization Energy -19.4516 kcal/mol@LB@Unfolding Energy - mRNA 0.236149 kcal/mol@LB@Unfolding Energy - sRNA 3.68511 kcal/mol@LB@@LB@Position - mRNA 18 -- 81@LB@Position - sRNA 44 -- 90@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 155 -- 161@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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