Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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	Additional homologs
167	0.00885	0.1781	b0241	phoE	-12.37	0.054121	1 -- 29	1 -- 31	outer membrane phosphoporin protein E	b0929 b2215 b1377	______________1____________________________________30\n______________\|____________________________________\|\n___________5'-___A___________UGCGC___A_____________AAGCC...AUG-3'\n______________AGC_UGGCGUUUUGU_____GGG_________UCAGC\n______________\|\|\|_\|:\|\|:\|\|\|\|:\|_____\|\|\|_________\|\|\|\|\|\n______________UCG_AUCGUAAAAUA_____CCC_________AGUCG\n3'-UUU...CCAUG_______________________AAUACAAAA_____-5'\n_____________\|____________________________________\|\n_____________32___________________________________1\n	9 -- 15	18 -- 24	-21.8929 kcal/mol	8.03382 kcal/mol	1.48722 kcal/mol	1 30@LB@ \| \|@LB@ 5'- A UGCGC A AAGCC...AUG-3'@LB@ AGC UGGCGUUUUGU GGG UCAGC@LB@ \|\|\| \|:\|\|:\|\|\|\|:\| \|\|\| \|\|\|\|\|@LB@ UCG AUCGUAAAAUA CCC AGUCG@LB@3'-UUU...CCAUG AAUACAAAA -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -12.37 kcal/mol@LB@Hybridization Energy -21.8929 kcal/mol@LB@Unfolding Energy - mRNA 8.03382 kcal/mol@LB@Unfolding Energy - sRNA 1.48722 kcal/mol@LB@@LB@Position - mRNA 1 -- 29@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 18 -- 24@LB@
107	0.004137	0.1296	b2164	psuT	-12.74	0.044381	225 -- 254	21 -- 50	putative nucleoside transporter	b2161	_____________224_______________________________255\n_____________\|_________________________________\|\n5'-CUG...UUGUG____U______GUUA________A_________CUGUU...GAG-3'\n______________GGGA_GGUGGU____CUGG__CA__UAGCAUUU\n______________:\|\|\|_\|\|\|\|\|\|____\|\|\|\|__\|\|__\|\|\|\|\|\|\|\|\n______________UCCU_CCACCA____GACC__GU__AUCGUAAA\n3'-UUU...CCGAU___________AG______AU__CG________AUACC...UCG-5'\n_____________\|_________________________________\|\n_____________51________________________________20\n	248 -- 254	21 -- 27	-28.746 kcal/mol	11.392 kcal/mol	4.61445 kcal/mol	224 255@LB@ \| \|@LB@5'-CUG...UUGUG U GUUA A CUGUU...GAG-3'@LB@ GGGA GGUGGU CUGG CA UAGCAUUU@LB@ :\|\|\| \|\|\|\|\|\| \|\|\|\| \|\| \|\|\|\|\|\|\|\|@LB@ UCCU CCACCA GACC GU AUCGUAAA@LB@3'-UUU...CCGAU AG AU CG AUACC...UCG-5'@LB@ \| \|@LB@ 51 20@LB@@LB@@LB@Energy -12.74 kcal/mol@LB@Hybridization Energy -28.746 kcal/mol@LB@Unfolding Energy - mRNA 11.392 kcal/mol@LB@Unfolding Energy - sRNA 4.61445 kcal/mol@LB@@LB@Position - mRNA 225 -- 254@LB@Position - sRNA 21 -- 50@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 21 -- 27@LB@
105	0.003867	0.1238	b0716	ybgO	-11.28	0.093728	281 -- 296	25 -- 40	putative fimbrial protein	b3048	_____________280______________297\n_____________\|________________\|\n5'-GCC...UGCUA__________U_____GGCG-3'\n______________UUUUGGUACA_CUGGU\n______________\|::\|\|\|\|\|\|\|_\|\|:\|:\n______________AGGACCAUGU_GAUCG\n3'-UUU...CACCA__________C_____UAAAA...UCG-5'\n_____________\|________________\|\n_____________41_______________24\n	284 -- 290	31 -- 37	-18.2853 kcal/mol	2.44789 kcal/mol	4.55365 kcal/mol	280 297@LB@ \| \|@LB@5'-GCC...UGCUA U GGCG-3'@LB@ UUUUGGUACA CUGGU@LB@ \|::\|\|\|\|\|\|\| \|\|:\|:@LB@ AGGACCAUGU GAUCG@LB@3'-UUU...CACCA C UAAAA...UCG-5'@LB@ \| \|@LB@ 41 24@LB@@LB@@LB@Energy -11.28 kcal/mol@LB@Hybridization Energy -18.2853 kcal/mol@LB@Unfolding Energy - mRNA 2.44789 kcal/mol@LB@Unfolding Energy - sRNA 4.55365 kcal/mol@LB@@LB@Position - mRNA 281 -- 296@LB@Position - sRNA 25 -- 40@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 31 -- 37@LB@
99	0.003591	0.1219	b0533	sfmH	-7.90	0.364135	113 -- 140	1 -- 34	FimA homolog function unknown	b3145 b0941	_____________112________________________________141\n_____________\|__________________________________\|\n5'-GAC...AAGCU______A___CGUCACU_________________AGUUU...AUA-3'\n______________UACAGC_AGC_________GUUA____UUUCGGC\n______________\|\|\|\|\|\|_\|\|\|_________\|\|\|\|____\|\|\|\|:\|\|\n______________AUGUCG_UCG_________CAAU____AAAGUCG\n3'-UUU...GGACC______A___UAAAAUACC____ACAA_______-5'\n_____________\|_________________________________\|\n_____________35________________________________1\n	134 -- 140	1 -- 7	-18.6412 kcal/mol	9.24123 kcal/mol	1.49507 kcal/mol	112 141@LB@ \| \|@LB@5'-GAC...AAGCU A CGUCACU AGUUU...AUA-3'@LB@ UACAGC AGC GUUA UUUCGGC@LB@ \|\|\|\|\|\| \|\|\| \|\|\|\| \|\|\|\|:\|\|@LB@ AUGUCG UCG CAAU AAAGUCG@LB@3'-UUU...GGACC A UAAAAUACC ACAA -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -7.90 kcal/mol@LB@Hybridization Energy -18.6412 kcal/mol@LB@Unfolding Energy - mRNA 9.24123 kcal/mol@LB@Unfolding Energy - sRNA 1.49507 kcal/mol@LB@@LB@Position - mRNA 113 -- 140@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 1 -- 7@LB@
112	0.004445	0.1334	b0132	yadD	-7.85	0.370183	131 -- 161	16 -- 48	transposase_31 family protein	b3411 b2244 b2305	_____________130________________________________162\n_____________\|__________________________________\|\n5'-CCC...AUAAA_____________ACG_____GC__C__GAC___AUACU...UGG-3'\n______________GAGGUGG___CUG___AUAGC__GC_UU___UGG\n______________\|\|\|\|\|\|\|___\|\|\|___\|:\|\|\|__\|\|_\|\|___\|\|\|\n______________CUCCACC___GAC___UGUCG__CG_AA___ACC\n3'-UUU...GAUUC_______AAG___CA______AU__U__AAU___CAAUA...UCG-5'\n_____________\|__________________________________\|\n_____________49_________________________________15\n	131 -- 137	42 -- 48	-24.9925 kcal/mol	12.5665 kcal/mol	4.57255 kcal/mol	130 162@LB@ \| \|@LB@5'-CCC...AUAAA ACG GC C GAC AUACU...UGG-3'@LB@ GAGGUGG CUG AUAGC GC UU UGG@LB@ \|\|\|\|\|\|\| \|\|\| \|:\|\|\| \|\| \|\| \|\|\|@LB@ CUCCACC GAC UGUCG CG AA ACC@LB@3'-UUU...GAUUC AAG CA AU U AAU CAAUA...UCG-5'@LB@ \| \|@LB@ 49 15@LB@@LB@@LB@Energy -7.85 kcal/mol@LB@Hybridization Energy -24.9925 kcal/mol@LB@Unfolding Energy - mRNA 12.5665 kcal/mol@LB@Unfolding Energy - sRNA 4.57255 kcal/mol@LB@@LB@Position - mRNA 131 -- 161@LB@Position - sRNA 16 -- 48@LB@Position Seed - mRNA 131 -- 137@LB@Position Seed - sRNA 42 -- 48@LB@
81	0.002689	0.1082	b1498	ydeN	-15.88	0.005981	253 -- 275	21 -- 44	putative Ser-type periplasmic non-aryl sulfatase	b3678 b3801	_____________252______________________276\n_____________\|________________________\|\n5'-AUU...GAUAC___CA___________________GCUGC...UAA-3'\n______________UGG__UCUGGUAUGGCU_GCAUUU\n______________\|\|\|__:\|\|\|\|\|\|::\|\|\|_\|\|\|\|\|\|\n______________ACC__GGACCAUGUCGA_CGUAAA\n3'-UUU...CCUCC___AA____________U______AUACC...UCG-5'\n_____________\|________________________\|\n_____________45_______________________20\n	263 -- 269	28 -- 34	-26.8614 kcal/mol	6.42389 kcal/mol	4.55918 kcal/mol	252 276@LB@ \| \|@LB@5'-AUU...GAUAC CA GCUGC...UAA-3'@LB@ UGG UCUGGUAUGGCU GCAUUU@LB@ \|\|\| :\|\|\|\|\|\|::\|\|\| \|\|\|\|\|\|@LB@ ACC GGACCAUGUCGA CGUAAA@LB@3'-UUU...CCUCC AA U AUACC...UCG-5'@LB@ \| \|@LB@ 45 20@LB@@LB@@LB@Energy -15.88 kcal/mol@LB@Hybridization Energy -26.8614 kcal/mol@LB@Unfolding Energy - mRNA 6.42389 kcal/mol@LB@Unfolding Energy - sRNA 4.55918 kcal/mol@LB@@LB@Position - mRNA 253 -- 275@LB@Position - sRNA 21 -- 44@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 28 -- 34@LB@
161	0.008114	0.1694	b3656	yicI	-11.96	0.067144	124 -- 143	14 -- 37	putative alpha-glucosidase	b3878	_____________123______________________144\n_____________\|________________________\|\n5'-ACA...CGUUA___A_________UCA________AAACG...UGG-3'\n______________UGG_ACAGCUGGC_______GGGU\n______________\|\|\|_\|\|\|\|\|\|:\|\|_______\|\|\|\|\n______________ACC_UGUCGAUCG_______CCCA\n3'-UUU...CAAGG___A_________UAAAAUA____AUACA...UCG-5'\n_____________\|________________________\|\n_____________38_______________________13\n	130 -- 136	25 -- 31	-23.0355 kcal/mol	8.41802 kcal/mol	2.65978 kcal/mol	123 144@LB@ \| \|@LB@5'-ACA...CGUUA A UCA AAACG...UGG-3'@LB@ UGG ACAGCUGGC GGGU@LB@ \|\|\| \|\|\|\|\|\|:\|\| \|\|\|\|@LB@ ACC UGUCGAUCG CCCA@LB@3'-UUU...CAAGG A UAAAAUA AUACA...UCG-5'@LB@ \| \|@LB@ 38 13@LB@@LB@@LB@Energy -11.96 kcal/mol@LB@Hybridization Energy -23.0355 kcal/mol@LB@Unfolding Energy - mRNA 8.41802 kcal/mol@LB@Unfolding Energy - sRNA 2.65978 kcal/mol@LB@@LB@Position - mRNA 124 -- 143@LB@Position - sRNA 14 -- 37@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 25 -- 31@LB@
78	0.002256	0.09621	b0509	glxR	-14.00	0.021344	191 -- 236	14 -- 48	tartronate semialdehyde reductase NADH-dependent	b3882 b3125	_____________190______________________________________________237\n_____________\|________________________________________________\|\n5'-AGG...UAAAA_____UAAUUAUGAAA____GAUUUAU_____UA______________ACACC...CGG-3'\n______________GAGGU___________CUGG_______UGGCU__GGCAU__UAUGGGU\n______________\|\|\|\|\|___________\|\|\|\|_______::\|\|\|__:\|\|\|\|__\|\|\|\|\|\|\|\n______________CUCCA___________GACC_______GUCGA__UCGUA__AUACCCA\n3'-UUU...GAUUC_____CCAAG__________AU_________________AA_______AUACA...UCG-5'\n_____________\|________________________________________________\|\n_____________49_______________________________________________13\n	230 -- 236	14 -- 20	-26.1649 kcal/mol	7.59311 kcal/mol	4.57384 kcal/mol	190 237@LB@ \| \|@LB@5'-AGG...UAAAA UAAUUAUGAAA GAUUUAU UA ACACC...CGG-3'@LB@ GAGGU CUGG UGGCU GGCAU UAUGGGU@LB@ \|\|\|\|\| \|\|\|\| ::\|\|\| :\|\|\|\| \|\|\|\|\|\|\|@LB@ CUCCA GACC GUCGA UCGUA AUACCCA@LB@3'-UUU...GAUUC CCAAG AU AA AUACA...UCG-5'@LB@ \| \|@LB@ 49 13@LB@@LB@@LB@Energy -14.00 kcal/mol@LB@Hybridization Energy -26.1649 kcal/mol@LB@Unfolding Energy - mRNA 7.59311 kcal/mol@LB@Unfolding Energy - sRNA 4.57384 kcal/mol@LB@@LB@Position - mRNA 191 -- 236@LB@Position - sRNA 14 -- 48@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 14 -- 20@LB@
75	0.002192	0.09621	b3950	frwB	-15.16	0.010002	30 -- 54	11 -- 46	putative enzyme IIB component of PTS	b3899	_____________29___________________________________55\n_____________\|____________________________________\|\n5'-GCA...CUGCC_______GAA________A_________________AUCGC...GGG-3'\n______________GGUGGUU________GGC_AGC______UGGGUUAU\n______________\|\|\|\|\|\|\|________:\|\|_\|\|\|______\|\|\|\|\|\|\|\|\n______________CCACCAA________UCG_UCG______ACCCAAUA\n3'-UUU...UUCCU_______GGACCAUG___A___UAAAAU________CAAAA...UCG-5'\n_____________\|____________________________________\|\n_____________47___________________________________10\n	48 -- 54	11 -- 17	-24.5661 kcal/mol	4.81447 kcal/mol	4.59143 kcal/mol	29 55@LB@ \| \|@LB@5'-GCA...CUGCC GAA A AUCGC...GGG-3'@LB@ GGUGGUU GGC AGC UGGGUUAU@LB@ \|\|\|\|\|\|\| :\|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ CCACCAA UCG UCG ACCCAAUA@LB@3'-UUU...UUCCU GGACCAUG A UAAAAU CAAAA...UCG-5'@LB@ \| \|@LB@ 47 10@LB@@LB@@LB@Energy -15.16 kcal/mol@LB@Hybridization Energy -24.5661 kcal/mol@LB@Unfolding Energy - mRNA 4.81447 kcal/mol@LB@Unfolding Energy - sRNA 4.59143 kcal/mol@LB@@LB@Position - mRNA 30 -- 54@LB@Position - sRNA 11 -- 46@LB@Position Seed - mRNA 48 -- 54@LB@Position Seed - sRNA 11 -- 17@LB@
1	0	0	b3824	rhtB	-9.47	0.207720	26 -- 71	1 -- 43	homoserine homoserine lactone and S-methyl-methionine efflux pump		_____________25_________________________________________________72\n_____________\|__________________________________________________\|\n5'-ACG...UCAGC___C__A____AAAA_____AAAC_______CUCU_________CC____CUUUU...ACC-3'\n______________GGU_CC_UGGU____GCAGC____GCGUUUU________UGUUU__CAGU\n______________\|\|\|_\|\|_\|\|\|\|____:\|\|\|\|____\|\|:\|\|\|\|________\|\|\|\|\|__\|\|\|:\n______________CCA_GG_ACCA____UGUCG____CGUAAAA________ACAAA__GUCG\n3'-UUU...CUCCA___A________________AU_________UACCCAAU_____AA____-5'\n_____________\|_________________________________________________\|\n_____________44________________________________________________1\n	50 -- 56	20 -- 26	-25.7164 kcal/mol	11.6412 kcal/mol	4.6088 kcal/mol	25 72@LB@ \| \|@LB@5'-ACG...UCAGC C A AAAA AAAC CUCU CC CUUUU...ACC-3'@LB@ GGU CC UGGU GCAGC GCGUUUU UGUUU CAGU@LB@ \|\|\| \|\| \|\|\|\| :\|\|\|\| \|\|:\|\|\|\| \|\|\|\|\| \|\|\|:@LB@ CCA GG ACCA UGUCG CGUAAAA ACAAA GUCG@LB@3'-UUU...CUCCA A AU UACCCAAU AA -5'@LB@ \| \|@LB@ 44 1@LB@@LB@@LB@Energy -9.47 kcal/mol@LB@Hybridization Energy -25.7164 kcal/mol@LB@Unfolding Energy - mRNA 11.6412 kcal/mol@LB@Unfolding Energy - sRNA 4.6088 kcal/mol@LB@@LB@Position - mRNA 26 -- 71@LB@Position - sRNA 1 -- 43@LB@Position Seed - mRNA 50 -- 56@LB@Position Seed - sRNA 20 -- 26@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)

Job resubmission

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

service.

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching