Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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_000913 Escherichia coli str. K-12 substr. MG1655

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
61	0.0009386	0.05413	b0574	cusB	-12.39	0.007718	27 -- 84	1 -- 59	copper/silver efflux system membrane fusion protein	_____________26_____________________________________________________________85\n_____________\|______________________________________________________________\|\n5'-AAA...AUCAC______________CC_____CU__C_G____U__CCAU___C______A_________C__AGACG...AAA-3'\n______________GAUCCGAUUGC_UG__GUGAA__GG_C_GAGA_GA____GCG_UUUACC_UC___ACCC_GC\n______________:\|\|\|\|\|\|\|\|:\|_\|\|__\|\|:\|\|__\|\|_\|_\|\|:\|_\|\|____:\|:_:\|\|\|\|\|_\|\|___\|\|\|\|_:\|\n______________UUAGGCUAAUG_AC__CAUUU__CC_G_CUUU_CU____UGU_GAAUGG_AG___UGGG_UG\n3'-AUU...UCGGU___________C__UU_____U___A_A_______AUCU___A_________ACA____A__-5'\n_____________\|_____________________________________________________________\|\n_____________60____________________________________________________________1\n	31 -- 37	49 -- 55	-39.7476 kcal/mol	14.6812 kcal/mol	12.7027 kcal/mol	26 85@LB@ \| \|@LB@5'-AAA...AUCAC CC CU C G U CCAU C A C AGACG...AAA-3'@LB@ GAUCCGAUUGC UG GUGAA GG C GAGA GA GCG UUUACC UC ACCC GC@LB@ :\|\|\|\|\|\|\|\|:\| \|\| \|\|:\|\| \|\| \| \|\|:\| \|\| :\|: :\|\|\|\|\| \|\| \|\|\|\| :\|@LB@ UUAGGCUAAUG AC CAUUU CC G CUUU CU UGU GAAUGG AG UGGG UG@LB@3'-AUU...UCGGU C UU U A A AUCU A ACA A -5'@LB@ \| \|@LB@ 60 1@LB@@LB@@LB@Energy -12.39 kcal/mol@LB@Hybridization Energy -39.7476 kcal/mol@LB@Unfolding Energy - mRNA 14.6812 kcal/mol@LB@Unfolding Energy - sRNA 12.7027 kcal/mol@LB@@LB@Position - mRNA 27 -- 84@LB@Position - sRNA 1 -- 59@LB@Position Seed - mRNA 31 -- 37@LB@Position Seed - sRNA 49 -- 55@LB@
62	0.001059	0.05856	b3927	glpF	-11.40	0.016677	192 -- 203	48 -- 59	glycerol facilitator	_____________191__________204\n_____________\|____________\|\n5'-GAU...UUCAG____________AGUCA...AAG-3'\n______________GAUCCGAUUAUG\n______________:\|\|\|\|\|\|\|\|\|:\|\n______________UUAGGCUAAUGC\n3'-AUU...UCGGU____________ACUUC...AUG-5'\n_____________\|____________\|\n_____________60___________47\n	197 -- 203	48 -- 54	-15.6898 kcal/mol	2.7066 kcal/mol	1.55995 kcal/mol	191 204@LB@ \| \|@LB@5'-GAU...UUCAG AGUCA...AAG-3'@LB@ GAUCCGAUUAUG@LB@ :\|\|\|\|\|\|\|\|\|:\|@LB@ UUAGGCUAAUGC@LB@3'-AUU...UCGGU ACUUC...AUG-5'@LB@ \| \|@LB@ 60 47@LB@@LB@@LB@Energy -11.40 kcal/mol@LB@Hybridization Energy -15.6898 kcal/mol@LB@Unfolding Energy - mRNA 2.7066 kcal/mol@LB@Unfolding Energy - sRNA 1.55995 kcal/mol@LB@@LB@Position - mRNA 192 -- 203@LB@Position - sRNA 48 -- 59@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 48 -- 54@LB@
63	0.001074	0.05856	b0448	mdlA	-11.87	0.011698	129 -- 162	4 -- 28	putative multidrug ABC transporter ATPase	_____________128________________________________163\n_____________\|__________________________________\|\n5'-UGG...UUCGC_________GA__AAAUACACC______U_____AUCGA...UGG-3'\n______________GAUGGAACA__UU_________ACUUCU_UACCC\n______________\|\|\|:\|\|\|\|\|__\|\|_________\|\|:\|\|\|_\|\|\|\|\|\n______________CUAUCUUGU__AA_________UGGAGA_AUGGG\n3'-AUU...ACUUU_________AG_________________C_____AUG-5'\n_____________\|__________________________________\|\n_____________29_________________________________3\n	131 -- 137	20 -- 26	-24.4185 kcal/mol	4.52675 kcal/mol	8.04825 kcal/mol	128 163@LB@ \| \|@LB@5'-UGG...UUCGC GA AAAUACACC U AUCGA...UGG-3'@LB@ GAUGGAACA UU ACUUCU UACCC@LB@ \|\|\|:\|\|\|\|\| \|\| \|\|:\|\|\| \|\|\|\|\|@LB@ CUAUCUUGU AA UGGAGA AUGGG@LB@3'-AUU...ACUUU AG C AUG-5'@LB@ \| \|@LB@ 29 3@LB@@LB@@LB@Energy -11.87 kcal/mol@LB@Hybridization Energy -24.4185 kcal/mol@LB@Unfolding Energy - mRNA 4.52675 kcal/mol@LB@Unfolding Energy - sRNA 8.04825 kcal/mol@LB@@LB@Position - mRNA 129 -- 162@LB@Position - sRNA 4 -- 28@LB@Position Seed - mRNA 131 -- 137@LB@Position Seed - sRNA 20 -- 26@LB@
64	0.001083	0.05856	b3471	yhhQ	-11.41	0.016564	49 -- 60	44 -- 55	DUF165 family inner membrane protein	_____________48___________61\n_____________\|____________\|\n5'-AAA...GUUAA____________AAUUA...UUC-3'\n______________CGAUUGCGUGAA\n______________\|\|\|\|\|:\|\|\|\|\|\|\n______________GCUAAUGCACUU\n3'-AUU...UUUAG____________CAUUU...AUG-5'\n_____________\|____________\|\n_____________56___________43\n	54 -- 60	44 -- 50	-16.5289 kcal/mol	2.50651 kcal/mol	2.62518 kcal/mol	48 61@LB@ \| \|@LB@5'-AAA...GUUAA AAUUA...UUC-3'@LB@ CGAUUGCGUGAA@LB@ \|\|\|\|\|:\|\|\|\|\|\|@LB@ GCUAAUGCACUU@LB@3'-AUU...UUUAG CAUUU...AUG-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -11.41 kcal/mol@LB@Hybridization Energy -16.5289 kcal/mol@LB@Unfolding Energy - mRNA 2.50651 kcal/mol@LB@Unfolding Energy - sRNA 2.62518 kcal/mol@LB@@LB@Position - mRNA 49 -- 60@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 44 -- 50@LB@
65	0.001093	0.05856	b1519	tam	-11.83	0.011992	187 -- 231	1 -- 50	trans-aconitate methyltransferase	_____________186____________________________________________________232\n_____________\|______________________________________________________\|\n5'-UUU...CGCUG_____________AAAU______C_________C__________U___A_____ACUUU...AAU-3'\n______________ACG_GGAGUAAAA____GUCUGA____UGGAAC______CCUCU_UAU_UCUAC\n______________\|\|\|_\|:\|\|\|\|\|\|\|____\|\|\|\|\|\|____\|:\|\|\|\|______\|\|\|\|\|_\|\|:_:\|\|\|\|\n______________UGC_CUUCAUUUU____CAGACU____AUCUUG______GGAGA_AUG_GGAUG\n3'-AUU...GCUAA___A_________C_________UUCU______UAGAAU_____C_________-5'\n_____________\|_____________________________________________________\|\n_____________51____________________________________________________1\n	191 -- 197	39 -- 45	-32.7669 kcal/mol	8.27841 kcal/mol	12.6772 kcal/mol	186 232@LB@ \| \|@LB@5'-UUU...CGCUG AAAU C C U A ACUUU...AAU-3'@LB@ ACG GGAGUAAAA GUCUGA UGGAAC CCUCU UAU UCUAC@LB@ \|\|\| \|:\|\|\|\|\|\|\| \|\|\|\|\|\| \|:\|\|\|\| \|\|\|\|\| \|\|: :\|\|\|\|@LB@ UGC CUUCAUUUU CAGACU AUCUUG GGAGA AUG GGAUG@LB@3'-AUU...GCUAA A C UUCU UAGAAU C -5'@LB@ \| \|@LB@ 51 1@LB@@LB@@LB@Energy -11.83 kcal/mol@LB@Hybridization Energy -32.7669 kcal/mol@LB@Unfolding Energy - mRNA 8.27841 kcal/mol@LB@Unfolding Energy - sRNA 12.6772 kcal/mol@LB@@LB@Position - mRNA 187 -- 231@LB@Position - sRNA 1 -- 50@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 39 -- 45@LB@
66	0.001146	0.05856	b1657	ydhP	-3.95	0.782289	131 -- 139	49 -- 57	putative MFS transporter inner membrane protein	_____________130_______140\n_____________\|_________\|\n5'-UCG...UUUUU_G_______UGUCA...GCG-3'\n______________U_UGAUUGC\n______________\|_:\|\|\|\|:\|\n______________A_GCUAAUG\n3'-AUU...GGUUU_G_______CACUU...AUG-5'\n_____________\|_________\|\n_____________58________48\n	133 -- 139	49 -- 55	-6.30818 kcal/mol	2.04371 kcal/mol	0.318327 kcal/mol	130 140@LB@ \| \|@LB@5'-UCG...UUUUU G UGUCA...GCG-3'@LB@ U UGAUUGC@LB@ \| :\|\|\|\|:\|@LB@ A GCUAAUG@LB@3'-AUU...GGUUU G CACUU...AUG-5'@LB@ \| \|@LB@ 58 48@LB@@LB@@LB@Energy -3.95 kcal/mol@LB@Hybridization Energy -6.30818 kcal/mol@LB@Unfolding Energy - mRNA 2.04371 kcal/mol@LB@Unfolding Energy - sRNA 0.318327 kcal/mol@LB@@LB@Position - mRNA 131 -- 139@LB@Position - sRNA 49 -- 57@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 49 -- 55@LB@
67	0.001147	0.05856	b2319	usg	-10.96	0.023185	203 -- 221	18 -- 36	putative semialdehyde dehydrogenase	_____________202_________________222\n_____________\|___________________\|\n5'-GAG...ACCAU_________C_________GCCGU...AAA-3'\n______________GUCUGAAGG_UGGAACAUU\n______________\|\|\|\|\|\|\|:\|_\|:\|\|\|\|\|\|:\n______________CAGACUUUC_AUCUUGUAG\n3'-AUU...UUUUC_________U_________AAUGG...AUG-5'\n_____________\|___________________\|\n_____________37__________________17\n	215 -- 221	18 -- 24	-22.956 kcal/mol	5.32254 kcal/mol	6.60045 kcal/mol	202 222@LB@ \| \|@LB@5'-GAG...ACCAU C GCCGU...AAA-3'@LB@ GUCUGAAGG UGGAACAUU@LB@ \|\|\|\|\|\|\|:\| \|:\|\|\|\|\|\|:@LB@ CAGACUUUC AUCUUGUAG@LB@3'-AUU...UUUUC U AAUGG...AUG-5'@LB@ \| \|@LB@ 37 17@LB@@LB@@LB@Energy -10.96 kcal/mol@LB@Hybridization Energy -22.956 kcal/mol@LB@Unfolding Energy - mRNA 5.32254 kcal/mol@LB@Unfolding Energy - sRNA 6.60045 kcal/mol@LB@@LB@Position - mRNA 203 -- 221@LB@Position - sRNA 18 -- 36@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 18 -- 24@LB@
68	0.001174	0.05856	b1253	yciA	-8.30	0.130708	128 -- 145	3 -- 21	acyl-CoA esterase	_____________127__________________146\n_____________\|____________________\|\n5'-UUU...CGCUG______________UC____CAGGA...GGU-3'\n______________UAUCU__CCUCUGU__UCCU\n______________:\|\|\|\|__\|\|\|\|\|\|\|__:\|\|\|\n______________GUAGA__GGAGACA__GGGA\n3'-AUU...AUCUU_____AU_______U_____UG-5'\n_____________\|____________________\|\n_____________22___________________2\n	133 -- 139	8 -- 14	-17.321 kcal/mol	1.04882 kcal/mol	7.99052 kcal/mol	127 146@LB@ \| \|@LB@5'-UUU...CGCUG UC CAGGA...GGU-3'@LB@ UAUCU CCUCUGU UCCU@LB@ :\|\|\|\| \|\|\|\|\|\|\| :\|\|\|@LB@ GUAGA GGAGACA GGGA@LB@3'-AUU...AUCUU AU U UG-5'@LB@ \| \|@LB@ 22 2@LB@@LB@@LB@Energy -8.30 kcal/mol@LB@Hybridization Energy -17.321 kcal/mol@LB@Unfolding Energy - mRNA 1.04882 kcal/mol@LB@Unfolding Energy - sRNA 7.99052 kcal/mol@LB@@LB@Position - mRNA 128 -- 145@LB@Position - sRNA 3 -- 21@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 8 -- 14@LB@
69	0.001182	0.05856	b2962	yggX	-12.92	0.004967	226 -- 272	1 -- 57	oxidative damage protective factor for iron-sulfur proteins	_____________225________________________________________________________273\n_____________\|__________________________________________________________\|\n5'-UCA...UACUU___UGCA________C____________________G_______AG________CG__GAGCU...AGA-3'\n______________UCC____ACGUGAAG_AGAAGGUC__________AG_AUUUU_C__CUGUACCC__GC\n______________\|\|\|____\|\|\|\|\|\|\|\|_\|:\|\|\|\|\|\|__________\|:_\|\|:\|\|_\|__\|\|\|\|\|\|\|\|__:\|\n______________AGG____UGCACUUC_UUUUCCAG__________UU_UAGAA_G__GACAUGGG__UG\n3'-AUU...GGUUU___CUAA________A________ACUUUCUAUC__G_____U_GA________A___-5'\n_____________\|_________________________________________________________\|\n_____________58________________________________________________________1\n	262 -- 268	4 -- 10	-42.3698 kcal/mol	16.7751 kcal/mol	12.7026 kcal/mol	225 273@LB@ \| \|@LB@5'-UCA...UACUU UGCA C G AG CG GAGCU...AGA-3'@LB@ UCC ACGUGAAG AGAAGGUC AG AUUUU C CUGUACCC GC@LB@ \|\|\| \|\|\|\|\|\|\|\| \|:\|\|\|\|\|\| \|: \|\|:\|\| \| \|\|\|\|\|\|\|\| :\|@LB@ AGG UGCACUUC UUUUCCAG UU UAGAA G GACAUGGG UG@LB@3'-AUU...GGUUU CUAA A ACUUUCUAUC G U GA A -5'@LB@ \| \|@LB@ 58 1@LB@@LB@@LB@Energy -12.92 kcal/mol@LB@Hybridization Energy -42.3698 kcal/mol@LB@Unfolding Energy - mRNA 16.7751 kcal/mol@LB@Unfolding Energy - sRNA 12.7026 kcal/mol@LB@@LB@Position - mRNA 226 -- 272@LB@Position - sRNA 1 -- 57@LB@Position Seed - mRNA 262 -- 268@LB@Position Seed - sRNA 4 -- 10@LB@
70	0.001199	0.05856	b0954	fabA	-10.37	0.035200	228 -- 254	4 -- 31	beta-hydroxydecanoyl thioester dehydrase	_____________227__________________________255\n_____________\|____________________________\|\n5'-GUG...AUACA_________C_U___________GU_G_GGUGA...ACA-3'\n______________AAAGA_AGA_C_UCUUGCCUCUG__C_C\n______________\|\|\|\|\|_\|\|\|_\|_\|\|\|\|:\|\|\|\|\|\|__\|_\|\n______________UUUCU_UCU_G_AGAAUGGAGAC__G_G\n3'-AUU...CAGAC_____A___U_U___________AU_G_AUG-5'\n_____________\|____________________________\|\n_____________32___________________________3\n	243 -- 249	9 -- 15	-26.2676 kcal/mol	7.86183 kcal/mol	8.05676 kcal/mol	227 255@LB@ \| \|@LB@5'-GUG...AUACA C U GU G GGUGA...ACA-3'@LB@ AAAGA AGA C UCUUGCCUCUG C C@LB@ \|\|\|\|\| \|\|\| \| \|\|\|\|:\|\|\|\|\|\| \| \|@LB@ UUUCU UCU G AGAAUGGAGAC G G@LB@3'-AUU...CAGAC A U U AU G AUG-5'@LB@ \| \|@LB@ 32 3@LB@@LB@@LB@Energy -10.37 kcal/mol@LB@Hybridization Energy -26.2676 kcal/mol@LB@Unfolding Energy - mRNA 7.86183 kcal/mol@LB@Unfolding Energy - sRNA 8.05676 kcal/mol@LB@@LB@Position - mRNA 228 -- 254@LB@Position - sRNA 4 -- 31@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 9 -- 15@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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