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
15	0.000269	0.06194	stm3630	dppA	-21.81	0.008578	158 -- 199	51 -- 92	ABC transporter substrate-binding protein		_____________157_____________________________________200\n_____________\|_______________________________________\|\n5'-AUU...AGCCU______AGG___A__________________________AGAAG...AUU-3'\n______________UUGCAA___GCA_AACAACAU_ACAUCACAAUUG_GAGC\n______________\|\|\|\|\|\|___:\|\|_\|\|\|\|\|\|\|:_\|\|\|\|\|\|\|\|\|::\|_:\|\|\|\n______________AACGUU___UGU_UUGUUGUG_UGUAGUGUUGGC_UUCG\n3'-UUU...UGGUU____________G________U____________A____GUUUU...UCA-5'\n_____________\|_______________________________________\|\n_____________93______________________________________50\n	183 -- 189	63 -- 69	-36.2763 kcal/mol	6.81868 kcal/mol	11.5217 kcal/mol	157 200@LB@ \| \|@LB@5'-AUU...AGCCU AGG A AGAAG...AUU-3'@LB@ UUGCAA GCA AACAACAU ACAUCACAAUUG GAGC@LB@ \|\|\|\|\|\| :\|\| \|\|\|\|\|\|\|: \|\|\|\|\|\|\|\|\|::\| :\|\|\|@LB@ AACGUU UGU UUGUUGUG UGUAGUGUUGGC UUCG@LB@3'-UUU...UGGUU G U A GUUUU...UCA-5'@LB@ \| \|@LB@ 93 50@LB@@LB@@LB@Energy -21.81 kcal/mol@LB@Hybridization Energy -36.2763 kcal/mol@LB@Unfolding Energy - mRNA 6.81868 kcal/mol@LB@Unfolding Energy - sRNA 11.5217 kcal/mol@LB@@LB@Position - mRNA 158 -- 199@LB@Position - sRNA 51 -- 92@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 63 -- 69@LB@
46	0.001637	0.1267	stm2313	elaC	-17.21	0.051329	250 -- 300	51 -- 90	ribonuclease Z	stm1109	_____________249_____________________________________________301\n_____________\|_______________________________________________\|\n5'-UCG...CUCAC____UGUA________UUUAUUACAUCU________CAAC_______GGAG-3'\n______________GCAA____ACGGCAAU____________GCAACAUC____GCAGCCG\n______________\|\|\|\|____\|\|::\|\|\|:____________:\|\|\|\|\|\|\|____:\|\|:\|\|\|\n______________CGUU____UGUUGUUG____________UGUUGUAG____UGUUGGC\n3'-UUU...GUUAA____UG_________________________________________AUUCG...UCA-5'\n_____________\|_______________________________________________\|\n_____________91______________________________________________50\n	290 -- 296	62 -- 68	-28.5454 kcal/mol	7.10881 kcal/mol	8.62576 kcal/mol	249 301@LB@ \| \|@LB@5'-UCG...CUCAC UGUA UUUAUUACAUCU CAAC GGAG-3'@LB@ GCAA ACGGCAAU GCAACAUC GCAGCCG@LB@ \|\|\|\| \|\|::\|\|\|: :\|\|\|\|\|\|\| :\|\|:\|\|\|@LB@ CGUU UGUUGUUG UGUUGUAG UGUUGGC@LB@3'-UUU...GUUAA UG AUUCG...UCA-5'@LB@ \| \|@LB@ 91 50@LB@@LB@@LB@Energy -17.21 kcal/mol@LB@Hybridization Energy -28.5454 kcal/mol@LB@Unfolding Energy - mRNA 7.10881 kcal/mol@LB@Unfolding Energy - sRNA 8.62576 kcal/mol@LB@@LB@Position - mRNA 250 -- 300@LB@Position - sRNA 51 -- 90@LB@Position Seed - mRNA 290 -- 296@LB@Position Seed - sRNA 62 -- 68@LB@
110	0.005337	0.1728	stm1920	cheW	-12.58	0.277263	149 -- 192	51 -- 90	chemotaxis protein CheW		_____________148__________193\n_____________\|____________\|\n5'-GUC...UGAUU____________AAUAA...UCC-3'\n______________GAGUGAGAAGGG\n______________:\|\|\|\|\|:\|\|:\|\|\n______________UUCACUUUUUCC\n3'-UUU...UGUCC____________CAUCA...UCA-5'\n_____________\|____________\|\n_____________91___________50\n	188 -- 194	128 -- 134	-15.4894 kcal/mol	2.64754 kcal/mol	3.77328 kcal/mol	148 193@LB@ \| \|@LB@5'-GUC...UGAUU AAUAA...UCC-3'@LB@ GAGUGAGAAGGG@LB@ :\|\|\|\|\|:\|\|:\|\|@LB@ UUCACUUUUUCC@LB@3'-UUU...UGUCC CAUCA...UCA-5'@LB@ \| \|@LB@ 91 50@LB@@LB@@LB@Energy -12.58 kcal/mol@LB@Hybridization Energy -15.4894 kcal/mol@LB@Unfolding Energy - mRNA 2.64754 kcal/mol@LB@Unfolding Energy - sRNA 3.77328 kcal/mol@LB@@LB@Position - mRNA 149 -- 192@LB@Position - sRNA 51 -- 90@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 128 -- 134@LB@
17	0.0003055	0.06194	stm2694	N/A	-22.95	0.005498	261 -- 295	52 -- 90	Fels-2 prophage protein		_____________260_____________________________________296\n_____________\|_______________________________________\|\n5'-ACG...UAUCA_____________A_G____________AGU________UAUAA-3'\n______________GC___UACGACAA_A_AACGUUACAACC____GCCAAAA\n______________\|\|___:\|\|:\|\|\|\|_\|_\|\|\|:\|:\|\|\|\|\|\|____\|\|\|\|\|\|\|\n______________CG___GUGUUGUU_U_UUGUAGUGUUGG____CGGUUUU\n3'-UUU...GUUAA__UUU________G_G____________CAUU_______CGGGU...UCA-5'\n_____________\|_______________________________________\|\n_____________91______________________________________51\n	289 -- 295	52 -- 58	-35.4487 kcal/mol	2.51857 kcal/mol	14.0353 kcal/mol	260 296@LB@ \| \|@LB@5'-ACG...UAUCA A G AGU UAUAA-3'@LB@ GC UACGACAA A AACGUUACAACC GCCAAAA@LB@ \|\| :\|\|:\|\|\|\| \| \|\|\|:\|:\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ CG GUGUUGUU U UUGUAGUGUUGG CGGUUUU@LB@3'-UUU...GUUAA UUU G G CAUU CGGGU...UCA-5'@LB@ \| \|@LB@ 91 51@LB@@LB@@LB@Energy -22.95 kcal/mol@LB@Hybridization Energy -35.4487 kcal/mol@LB@Unfolding Energy - mRNA 2.51857 kcal/mol@LB@Unfolding Energy - sRNA 14.0353 kcal/mol@LB@@LB@Position - mRNA 261 -- 295@LB@Position - sRNA 52 -- 90@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 52 -- 58@LB@
67	0.003193	0.1596	stm0122	ftsI	-11.87	0.349270	199 -- 241	52 -- 90	peptidoglycan glycosyltransferase FtsI		_____________198_______________________242\n_____________\|_________________________\|\n5'-GUU...CGCGA____UUG_____UG___________CUGAU...UGG-3'\n______________UGCA___GACAU__AAUGGCGCAAC\n______________\|\|\|\|___:\|\|\|:__\|\|:::\|:\|\|\|\|\n______________ACGU___UUGUG__UUGUUGUGUUG\n3'-UUU...GGUUA_________________________UAGUG...UCA-5'\n_____________\|_________________________\|\n_____________91________________________51\n	62 -- 68	72 -- 78	-17.673 kcal/mol	4.85802 kcal/mol	3.80548 kcal/mol	198 242@LB@ \| \|@LB@5'-GUU...CGCGA UUG UG CUGAU...UGG-3'@LB@ UGCA GACAU AAUGGCGCAAC@LB@ \|\|\|\| :\|\|\|: \|\|:::\|:\|\|\|\|@LB@ ACGU UUGUG UUGUUGUGUUG@LB@3'-UUU...GGUUA UAGUG...UCA-5'@LB@ \| \|@LB@ 91 51@LB@@LB@@LB@Energy -11.87 kcal/mol@LB@Hybridization Energy -17.673 kcal/mol@LB@Unfolding Energy - mRNA 4.85802 kcal/mol@LB@Unfolding Energy - sRNA 3.80548 kcal/mol@LB@@LB@Position - mRNA 199 -- 241@LB@Position - sRNA 52 -- 90@LB@Position Seed - mRNA 62 -- 68@LB@Position Seed - sRNA 72 -- 78@LB@
104	0.005232	0.1728	stm0744	ybgC	-16.85	0.058772	132 -- 175	54 -- 90	tol-pal system-associated acyl-CoA thioesterase		_____________131_____________________________176\n_____________\|_______________________________\|\n5'-CUU...ACAAG____U____________UCUUGA________GGCGG...AAA-3'\n______________GCGA_AUACAACGGCAU______GGCAUUAC\n______________\|\|:\|_\|:\|\|\|\|\|::\|\|:______::\|\|\|:\|\|\n______________CGUU_UGUGUUGUUGUG______UUGUAGUG\n3'-UUU...GUUAA_______________________________UUGGC...UCA-5'\n_____________\|_______________________________\|\n_____________91______________________________53\n	156 -- 162	67 -- 73	-23.8418 kcal/mol	6.2547 kcal/mol	5.68203 kcal/mol	131 176@LB@ \| \|@LB@5'-CUU...ACAAG U UCUUGA GGCGG...AAA-3'@LB@ GCGA AUACAACGGCAU GGCAUUAC@LB@ \|\|:\| \|:\|\|\|\|\|::\|\|: ::\|\|\|:\|\|@LB@ CGUU UGUGUUGUUGUG UUGUAGUG@LB@3'-UUU...GUUAA UUGGC...UCA-5'@LB@ \| \|@LB@ 91 53@LB@@LB@@LB@Energy -16.85 kcal/mol@LB@Hybridization Energy -23.8418 kcal/mol@LB@Unfolding Energy - mRNA 6.2547 kcal/mol@LB@Unfolding Energy - sRNA 5.68203 kcal/mol@LB@@LB@Position - mRNA 132 -- 175@LB@Position - sRNA 54 -- 90@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 67 -- 73@LB@
142	0.007269	0.182	stm4341	frdC	-12.15	0.319206	131 -- 234	54 -- 160	fumarate reductase subunit C		_____________130__________________235\n_____________\|____________________\|\n5'-AGA...AGGAG_______________UA___GCAAA...CGG-3'\n______________UGC_AACAUGACGAC__AAC\n______________\|\|\|_\|\|\|\|::\|\|:\|\|__\|\|\|\n______________ACG_UUGUGUUGUUG__UUG\n3'-UUU...GGUUA___U___________UG___UAGUG...UCA-5'\n_____________\|____________________\|\n_____________161__________________53\n	202 -- 208	77 -- 83	-18.8897 kcal/mol	4.02107 kcal/mol	3.80548 kcal/mol	130 235@LB@ \| \|@LB@5'-AGA...AGGAG UA GCAAA...CGG-3'@LB@ UGC AACAUGACGAC AAC@LB@ \|\|\| \|\|\|\|::\|\|:\|\| \|\|\|@LB@ ACG UUGUGUUGUUG UUG@LB@3'-UUU...GGUUA U UG UAGUG...UCA-5'@LB@ \| \|@LB@ 161 53@LB@@LB@@LB@Energy -12.15 kcal/mol@LB@Hybridization Energy -18.8897 kcal/mol@LB@Unfolding Energy - mRNA 4.02107 kcal/mol@LB@Unfolding Energy - sRNA 3.80548 kcal/mol@LB@@LB@Position - mRNA 131 -- 234@LB@Position - sRNA 54 -- 160@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 77 -- 83@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@
154	0.008185	0.1845	stm3738	yigC	-11.16	0.433331	228 -- 246	55 -- 74	similar to E. coli orf hypothetical protein (AAC76670.1); Blastp hit to AAC76670.1 (223 aa) 94% identity in aa 19 - 223		_____________227__________________247\n_____________\|____________________\|\n5'-UAA...ACCUC_____________AC_____AAAUG...UUA-3'\n______________GCA__UACAAUAA__CACAA\n______________\|\|\|__:\|\|\|\|:\|\|__\|\|\|\|\|\n______________CGU__GUGUUGUU__GUGUU\n3'-UUU...GUUAA___UU_______________GUAGU...UCA-5'\n_____________\|____________________\|\n_____________75___________________54\n	27 -- 33	78 -- 84	-12.6647 kcal/mol	0.985902 kcal/mol	3.77104 kcal/mol	227 247@LB@ \| \|@LB@5'-UAA...ACCUC AC AAAUG...UUA-3'@LB@ GCA UACAAUAA CACAA@LB@ \|\|\| :\|\|\|\|:\|\| \|\|\|\|\|@LB@ CGU GUGUUGUU GUGUU@LB@3'-UUU...GUUAA UU GUAGU...UCA-5'@LB@ \| \|@LB@ 75 54@LB@@LB@@LB@Energy -11.16 kcal/mol@LB@Hybridization Energy -12.6647 kcal/mol@LB@Unfolding Energy - mRNA 0.985902 kcal/mol@LB@Unfolding Energy - sRNA 3.77104 kcal/mol@LB@@LB@Position - mRNA 228 -- 246@LB@Position - sRNA 55 -- 74@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 78 -- 84@LB@
159	0.008305	0.1845	stm3625	yhjV	-13.06	0.235438	203 -- 240	55 -- 86	transporter		_____________202________________________241\n_____________\|__________________________\|\n5'-UUA...UAUUU_____________CUCUA________CGACA...UCU-3'\n______________UGGGCAG__GGGG______UGCAGGA\n______________\|\|\|:\|\|\|__:\|\|\|______\|:\|\|\|\|\|\n______________ACCUGUC__UCCC______AUGUCCU\n3'-UUU...GUGAU_______UG____AUUUAC_______UCACU...UCA-5'\n_____________\|__________________________\|\n_____________87_________________________54\n	202 -- 208	139 -- 145	-24.2103 kcal/mol	7.6176 kcal/mol	3.71206 kcal/mol	202 241@LB@ \| \|@LB@5'-UUA...UAUUU CUCUA CGACA...UCU-3'@LB@ UGGGCAG GGGG UGCAGGA@LB@ \|\|\|:\|\|\| :\|\|\| \|:\|\|\|\|\|@LB@ ACCUGUC UCCC AUGUCCU@LB@3'-UUU...GUGAU UG AUUUAC UCACU...UCA-5'@LB@ \| \|@LB@ 87 54@LB@@LB@@LB@Energy -13.06 kcal/mol@LB@Hybridization Energy -24.2103 kcal/mol@LB@Unfolding Energy - mRNA 7.6176 kcal/mol@LB@Unfolding Energy - sRNA 3.71206 kcal/mol@LB@@LB@Position - mRNA 203 -- 240@LB@Position - sRNA 55 -- 86@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 139 -- 145@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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