Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
125	0.01377	0.3575	b2827	thyA	-14.98	0.027366	100 -- 109	16 -- 25	thymidylate synthetase		_____________99_____________________110\n_____________\|______________________\|\n5'-CAG...AAACA________A_____________AAAAG...AGA-3'\n______________GUAUUUAG__AC___UGAUGCA\n______________:\|\|:\|:\|\|__\|\|___\|\|\|\|\|\|\|\n______________UAUGAGUC__UG___ACUACGU\n3'-UUU...GUGGU________AG__UGU_______CCGUU...UAG-5'\n_____________\|______________________\|\n_____________26_____________________15\n	220 -- 226	160 -- 166	-15.3976 kcal/mol	3.04146 kcal/mol	4.80633 kcal/mol	99 110@LB@ \| \|@LB@5'-CAG...AAACA A AAAAG...AGA-3'@LB@ GUAUUUAG AC UGAUGCA@LB@ :\|\|:\|:\|\| \|\| \|\|\|\|\|\|\|@LB@ UAUGAGUC UG ACUACGU@LB@3'-UUU...GUGGU AG UGU CCGUU...UAG-5'@LB@ \| \|@LB@ 26 15@LB@@LB@@LB@Energy -14.98 kcal/mol@LB@Hybridization Energy -15.3976 kcal/mol@LB@Unfolding Energy - mRNA 3.04146 kcal/mol@LB@Unfolding Energy - sRNA 4.80633 kcal/mol@LB@@LB@Position - mRNA 100 -- 109@LB@Position - sRNA 16 -- 25@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 160 -- 166@LB@
55	0.005617	0.3247	b2829	ptsP	-11.41	0.146041	68 -- 133	122 -- 174	PEP-protein phosphotransferase enzyme I; GAF domain containing protein		______________68____________________________________________________________134\n______________\|_____________________________________________________________\|\n___________5'-_______UACACCAGA__U_____G_______AUG___AAGU_________C______G___GGUGG...UGG-3'\n______________CCAGCAG_________GU_UGA_C_GCUGGCG___GGU____UACUGGUAU_CGGUCA_ACA\n______________\|\|\|\|\|\|\|_________\|\|_\|:\|_\|_\|\|\|\|\|\|\|___\|:\|____:\|\|:::\|\|:_\|:\|\|\|\|_\|\|\|\n______________GGUCGUC_________CA_AUU_G_CGACCGC___CUA____GUGGUUAUG_GUCAGU_UGU\n___3'-UUUUUUUU__________________U___A_A_______CCA___AAAU_________A______G___ACUAC...UAG-5'\n_____________\|______________________________________________________________\|\n_____________175____________________________________________________________121\n	25 -- 31	197 -- 203	-46.8098 kcal/mol	17.4414 kcal/mol	18.4949 kcal/mol	68 134@LB@ \| \|@LB@ 5'- UACACCAGA U G AUG AAGU C G GGUGG...UGG-3'@LB@ CCAGCAG GU UGA C GCUGGCG GGU UACUGGUAU CGGUCA ACA@LB@ \|\|\|\|\|\|\| \|\| \|:\| \| \|\|\|\|\|\|\| \|:\| :\|\|:::\|\|: \|:\|\|\|\| \|\|\|@LB@ GGUCGUC CA AUU G CGACCGC CUA GUGGUUAUG GUCAGU UGU@LB@ 3'-UUUUUUUU U A A CCA AAAU A G ACUAC...UAG-5'@LB@ \| \|@LB@ 175 121@LB@@LB@@LB@Energy -11.41 kcal/mol@LB@Hybridization Energy -46.8098 kcal/mol@LB@Unfolding Energy - mRNA 17.4414 kcal/mol@LB@Unfolding Energy - sRNA 18.4949 kcal/mol@LB@@LB@Position - mRNA 68 -- 133@LB@Position - sRNA 122 -- 174@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 197 -- 203@LB@
184	0.02128	0.3833	b2831	mutH	-12.07	0.107608	142 -- 230	114 -- 189	methyl-directed mismatch repair protein		_____________141______________231\n_____________\|________________\|\n5'-UUC...CUGCG________________AUUGC...CGG-3'\n______________AAUAUUCGG_CACAUA\n______________\|\|\|\|:\|\|:\|_\|\|\|\|:\|\n______________UUAUGAGUC_GUGUGU\n3'-UUU...UGUGG_________A______ACUAC...UAG-5'\n_____________\|________________\|\n_____________190______________113\n	154 -- 160	174 -- 180	-15.1193 kcal/mol	2.199 kcal/mol	0.596263 kcal/mol	141 231@LB@ \| \|@LB@5'-UUC...CUGCG AUUGC...CGG-3'@LB@ AAUAUUCGG CACAUA@LB@ \|\|\|\|:\|\|:\| \|\|\|\|:\|@LB@ UUAUGAGUC GUGUGU@LB@3'-UUU...UGUGG A ACUAC...UAG-5'@LB@ \| \|@LB@ 190 113@LB@@LB@@LB@Energy -12.07 kcal/mol@LB@Hybridization Energy -15.1193 kcal/mol@LB@Unfolding Energy - mRNA 2.199 kcal/mol@LB@Unfolding Energy - sRNA 0.596263 kcal/mol@LB@@LB@Position - mRNA 142 -- 230@LB@Position - sRNA 114 -- 189@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 174 -- 180@LB@
41	0.003653	0.2912	b2842	kduD	-13.01	0.069205	14 -- 50	128 -- 174	2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase; KDG oxidoreductase; 20-ketosteroid reductase	b4266 b2774	_____________13_______________________________________________51\n_____________\|________________________________________________\|\n5'-CCG...AACGC______U____________________GAG____________G_____CCCGA...CGG-3'\n______________GUCAUA_UGUGAUGCA_______UAAC___CAG____GCGGU_AUCUC\n______________\|\|\|\|:\|_::\|\|\|\|\|\|\|_______:\|\|\|___\|\|\|____\|\|\|\|\|_\|\|\|:\|\n______________CAGUGU_GUACUACGU_______GUUG___GUC____CGCCA_UAGGG\n3'-UUU...UGAGU________________CCGUUCA____AAA___UUAA_____G_____UGACG...UAG-5'\n_____________\|________________________________________________\|\n_____________175______________________________________________127\n	23 -- 29	160 -- 166	-35.8105 kcal/mol	9.71011 kcal/mol	15.5834 kcal/mol	13 51@LB@ \| \|@LB@5'-CCG...AACGC U GAG G CCCGA...CGG-3'@LB@ GUCAUA UGUGAUGCA UAAC CAG GCGGU AUCUC@LB@ \|\|\|\|:\| ::\|\|\|\|\|\|\| :\|\|\| \|\|\| \|\|\|\|\| \|\|\|:\|@LB@ CAGUGU GUACUACGU GUUG GUC CGCCA UAGGG@LB@3'-UUU...UGAGU CCGUUCA AAA UUAA G UGACG...UAG-5'@LB@ \| \|@LB@ 175 127@LB@@LB@@LB@Energy -13.01 kcal/mol@LB@Hybridization Energy -35.8105 kcal/mol@LB@Unfolding Energy - mRNA 9.71011 kcal/mol@LB@Unfolding Energy - sRNA 15.5834 kcal/mol@LB@@LB@Position - mRNA 14 -- 50@LB@Position - sRNA 128 -- 174@LB@Position Seed - mRNA 23 -- 29@LB@Position Seed - sRNA 160 -- 166@LB@
167	0.01932	0.3812	b2912	fau	-13.57	0.053124	153 -- 189	109 -- 152	5-formyltetrahydrofolate cyclo-ligase family protein		_____________152__________190\n_____________\|____________\|\n5'-GAA...UGAGC____________GUCCG...UGG-3'\n______________AUGCUCGGUC_C\n______________\|\|:\|\|\|:\|\|\|_\|\n______________UAUGAGUCAG_G\n3'-UUU...GUGGU__________U_UGUAC...UAG-5'\n_____________\|____________\|\n_____________153__________108\n	31 -- 37	172 -- 178	-13.9133 kcal/mol	3.57919 kcal/mol	0.28482 kcal/mol	152 190@LB@ \| \|@LB@5'-GAA...UGAGC GUCCG...UGG-3'@LB@ AUGCUCGGUC C@LB@ \|\|:\|\|\|:\|\|\| \|@LB@ UAUGAGUCAG G@LB@3'-UUU...GUGGU U UGUAC...UAG-5'@LB@ \| \|@LB@ 153 108@LB@@LB@@LB@Energy -13.57 kcal/mol@LB@Hybridization Energy -13.9133 kcal/mol@LB@Unfolding Energy - mRNA 3.57919 kcal/mol@LB@Unfolding Energy - sRNA 0.28482 kcal/mol@LB@@LB@Position - mRNA 153 -- 189@LB@Position - sRNA 109 -- 152@LB@Position Seed - mRNA 31 -- 37@LB@Position Seed - sRNA 172 -- 178@LB@
135	0.01453	0.3575	b2934	cmtB	-15.85	0.018111	229 -- 275	145 -- 186	putative mannitol-specific enzyme IIA component of PTS		_____________228___________________276\n_____________\|_____________________\|\n5'-AUA...AGAAU_____________________UCAGC...UGG-3'\n______________CAUCAAU_CUCAGUUAUACAU\n______________\|\|:\|\|\|\|_\|\|\|\|\|\|:\|:\|\|\|\|\n______________GUGGUUA_GAGUCAGUGUGUA\n3'-UUU...AAAAU_______U_____________CUACG...UAG-5'\n_____________\|_____________________\|\n_____________187___________________144\n	242 -- 248	166 -- 172	-24.8158 kcal/mol	1.5387 kcal/mol	5.06797 kcal/mol	228 276@LB@ \| \|@LB@5'-AUA...AGAAU UCAGC...UGG-3'@LB@ CAUCAAU CUCAGUUAUACAU@LB@ \|\|:\|\|\|\| \|\|\|\|\|\|:\|:\|\|\|\|@LB@ GUGGUUA GAGUCAGUGUGUA@LB@3'-UUU...AAAAU U CUACG...UAG-5'@LB@ \| \|@LB@ 187 144@LB@@LB@@LB@Energy -15.85 kcal/mol@LB@Hybridization Energy -24.8158 kcal/mol@LB@Unfolding Energy - mRNA 1.5387 kcal/mol@LB@Unfolding Energy - sRNA 5.06797 kcal/mol@LB@@LB@Position - mRNA 229 -- 275@LB@Position - sRNA 145 -- 186@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 166 -- 172@LB@
71	0.00726	0.3408	b2944	yggI	-9.32	0.365111	156 -- 174	1 -- 18	Zn-dependent metalloprotease-related protein		_____________155_____________175\n_____________\|_______________\|\n5'-GAA...AGCCA________AG_____UUUUC...ACC-3'\n______________CCUCUUGC__UCAUC\n______________\|\|:\|\|\|\|\|__\|\|\|\|\|\n______________GGGGAACG__AGUAG\n3'-UUU...CCGUG________A______-5'\n_____________\|______________\|\n_____________19_____________1\n	161 -- 167	7 -- 13	-18.0684 kcal/mol	1.30619 kcal/mol	6.71812 kcal/mol	155 175@LB@ \| \|@LB@5'-GAA...AGCCA AG UUUUC...ACC-3'@LB@ CCUCUUGC UCAUC@LB@ \|\|:\|\|\|\|\| \|\|\|\|\|@LB@ GGGGAACG AGUAG@LB@3'-UUU...CCGUG A -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -9.32 kcal/mol@LB@Hybridization Energy -18.0684 kcal/mol@LB@Unfolding Energy - mRNA 1.30619 kcal/mol@LB@Unfolding Energy - sRNA 6.71812 kcal/mol@LB@@LB@Position - mRNA 156 -- 174@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 7 -- 13@LB@
116	0.01276	0.3575	b2989	yghU	-14.25	0.038539	247 -- 281	170 -- 208	putative S-transferase		_____________246______________________________________282\n_____________\|________________________________________\|\n5'-UUA...GGAUA____C________C_C_UU________________A____CCGGU...CGC-3'\n______________AAUC_GCUGGCGG_G_G______CGCCAAUA_UCA_UCGC\n______________\|\|\|\|_\|\|\|\|\|\|\|\|_\|_\|______\|:\|\|\|\|\|\|_\|\|\|_\|\|:\|\n______________UUAG_CGACCGCC_C_C______GUGGUUAU_AGU_AGUG\n3'-UUU...CCAUA____A__________A_UAAAAU________G___C____UGUAC...UAG-5'\n_____________\|________________________________________\|\n_____________209______________________________________169\n	267 -- 273	179 -- 185	-35.9489 kcal/mol	9.63265 kcal/mol	15.256 kcal/mol	246 282@LB@ \| \|@LB@5'-UUA...GGAUA C C C UU A CCGGU...CGC-3'@LB@ AAUC GCUGGCGG G G CGCCAAUA UCA UCGC@LB@ \|\|\|\| \|\|\|\|\|\|\|\| \| \| \|:\|\|\|\|\|\| \|\|\| \|\|:\|@LB@ UUAG CGACCGCC C C GUGGUUAU AGU AGUG@LB@3'-UUU...CCAUA A A UAAAAU G C UGUAC...UAG-5'@LB@ \| \|@LB@ 209 169@LB@@LB@@LB@Energy -14.25 kcal/mol@LB@Hybridization Energy -35.9489 kcal/mol@LB@Unfolding Energy - mRNA 9.63265 kcal/mol@LB@Unfolding Energy - sRNA 15.256 kcal/mol@LB@@LB@Position - mRNA 247 -- 281@LB@Position - sRNA 170 -- 208@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 179 -- 185@LB@
153	0.01719	0.3749	b2997	hybO	-10.59	0.212773	44 -- 57	176 -- 189	hydrogenase 2 small subunit		_____________43_________________58\n_____________\|__________________\|\n5'-CUC...AUUAA______________CU__CCUUC...GCA-3'\n______________UUACACUAAUGCUU__UC\n______________\|\|\|\|\|\|:\|\|\|:\|\|:__\|\|\n______________AAUGUGGUUAUGAG__AG\n3'-UUU...ACUAA______________UC__UGUGU...UAG-5'\n_____________\|__________________\|\n_____________190________________175\n	51 -- 57	176 -- 182	-17.3647 kcal/mol	0.828093 kcal/mol	4.66778 kcal/mol	43 58@LB@ \| \|@LB@5'-CUC...AUUAA CU CCUUC...GCA-3'@LB@ UUACACUAAUGCUU UC@LB@ \|\|\|\|\|\|:\|\|\|:\|\|: \|\|@LB@ AAUGUGGUUAUGAG AG@LB@3'-UUU...ACUAA UC UGUGU...UAG-5'@LB@ \| \|@LB@ 190 175@LB@@LB@@LB@Energy -10.59 kcal/mol@LB@Hybridization Energy -17.3647 kcal/mol@LB@Unfolding Energy - mRNA 0.828093 kcal/mol@LB@Unfolding Energy - sRNA 4.66778 kcal/mol@LB@@LB@Position - mRNA 44 -- 57@LB@Position - sRNA 176 -- 189@LB@Position Seed - mRNA 51 -- 57@LB@Position Seed - sRNA 176 -- 182@LB@
24	0.001922	0.2633	b3017	ftsP	-19.79	0.002953	203 -- 291	63 -- 135	septal ring component that protects the divisome from stress; multicopy suppressor of ftsI(Ts)		_____________202__________________________________________________________________________________________292\n_____________\|____________________________________________________________________________________________\|\n5'-GAC...AAUAU_________GUCG__________A_________C__G______CACU_____CA______GUUCCCCUGAAG____________________AGCAA...CGC-3'\n______________GUCA_CUCA____GCGUCAGUUC_UUCAGGCAU_GG__GAUUG____UUGUG__GGCGCU____________GCCAGCGCAGCCGG_GCAAC\n______________\|\|\|\|_\|:\|\|____\|\|:\|\|\|\|\|:\|_\|\|\|\|:\|\|\|\|_\|\|__:\|\|:\|____\|\|\|\|\|__\|:\|\|\|\|____________:\|\|\|:\|\|\|\|:\|\|:\|_:\|\|\|\|\n______________CAGU_GGGU____CGUAGUCAGG_AAGUUCGUA_CC__UUAGC____AACAC__CUGCGA____________UGGUUGCGUUGGUC_UGUUG\n3'-UUU...AACGC____A____GA_________________________AA______________C_______AU________________________G_____AAGCG...UAG-5'\n_____________\|____________________________________________________________________________________________\|\n_____________136__________________________________________________________________________________________62\n	278 -- 284	71 -- 77	-82.7619 kcal/mol	32.3928 kcal/mol	37.2191 kcal/mol	202 292@LB@ \| \|@LB@5'-GAC...AAUAU GUCG A C G CACU CA GUUCCCCUGAAG AGCAA...CGC-3'@LB@ GUCA CUCA GCGUCAGUUC UUCAGGCAU GG GAUUG UUGUG GGCGCU GCCAGCGCAGCCGG GCAAC@LB@ \|\|\|\| \|:\|\| \|\|:\|\|\|\|\|:\| \|\|\|\|:\|\|\|\| \|\| :\|\|:\| \|\|\|\|\| \|:\|\|\|\| :\|\|\|:\|\|\|\|:\|\|:\| :\|\|\|\|@LB@ CAGU GGGU CGUAGUCAGG AAGUUCGUA CC UUAGC AACAC CUGCGA UGGUUGCGUUGGUC UGUUG@LB@3'-UUU...AACGC A GA AA C AU G AAGCG...UAG-5'@LB@ \| \|@LB@ 136 62@LB@@LB@@LB@Energy -19.79 kcal/mol@LB@Hybridization Energy -82.7619 kcal/mol@LB@Unfolding Energy - mRNA 32.3928 kcal/mol@LB@Unfolding Energy - sRNA 37.2191 kcal/mol@LB@@LB@Position - mRNA 203 -- 291@LB@Position - sRNA 63 -- 135@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 71 -- 77@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