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
176	0.01994	0.3812	b2170	setB	-11.80	0.122017	181 -- 237	58 -- 116	lactose/glucose efflux system		_____________180____________238\n_____________\|______________\|\n5'-GCU...GAUCG______________AACUC...UGC-3'\n______________AC_CAG_CAUGCAU\n______________\|\|_\|\|\|_\|\|::\|\|\|\n______________UG_GUC_GUGUGUA\n3'-UUU...GGUUA__A___A_______CUACG...UAG-5'\n_____________\|______________\|\n_____________117____________57\n	200 -- 206	166 -- 172	-10.2756 kcal/mol	1.89616 kcal/mol	0.604817 kcal/mol	180 238@LB@ \| \|@LB@5'-GCU...GAUCG AACUC...UGC-3'@LB@ AC CAG CAUGCAU@LB@ \|\| \|\|\| \|\|::\|\|\|@LB@ UG GUC GUGUGUA@LB@3'-UUU...GGUUA A A CUACG...UAG-5'@LB@ \| \|@LB@ 117 57@LB@@LB@@LB@Energy -11.80 kcal/mol@LB@Hybridization Energy -10.2756 kcal/mol@LB@Unfolding Energy - mRNA 1.89616 kcal/mol@LB@Unfolding Energy - sRNA 0.604817 kcal/mol@LB@@LB@Position - mRNA 181 -- 237@LB@Position - sRNA 58 -- 116@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 166 -- 172@LB@
56	0.005619	0.3247	b2781	mazG	-9.54	0.334798	182 -- 193	141 -- 152	nucleoside triphosphate pyrophosphohydrolase		_____________181__________194\n_____________\|____________\|\n5'-UGA...ACCCG____________CAAUU...CGC-3'\n______________CAAUUUUCAGGA\n______________\|\|\|:\|\|\|\|\|\|:\|\n______________GUUGAAAGUCUU\n3'-UUU...GUUCA____________AACGC...UAG-5'\n_____________\|____________\|\n_____________153__________140\n	187 -- 193	141 -- 147	-13.182 kcal/mol	1.77322 kcal/mol	1.81388 kcal/mol	181 194@LB@ \| \|@LB@5'-UGA...ACCCG CAAUU...CGC-3'@LB@ CAAUUUUCAGGA@LB@ \|\|\|:\|\|\|\|\|\|:\|@LB@ GUUGAAAGUCUU@LB@3'-UUU...GUUCA AACGC...UAG-5'@LB@ \| \|@LB@ 153 140@LB@@LB@@LB@Energy -9.54 kcal/mol@LB@Hybridization Energy -13.182 kcal/mol@LB@Unfolding Energy - mRNA 1.77322 kcal/mol@LB@Unfolding Energy - sRNA 1.81388 kcal/mol@LB@@LB@Position - mRNA 182 -- 193@LB@Position - sRNA 141 -- 152@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 141 -- 147@LB@
162	0.01805	0.3749	b2499	purM	-13.07	0.067336	182 -- 195	13 -- 27	phosphoribosylaminoimidazole synthetase		_____________181______196\n_____________\|________\|\n__________5'-U________AUGGU...CGC-3'\n______________AUAUUCAG\n______________\|\|\|:\|\|\|\|\n______________UAUGAGUC\n3'-UUU...GUGGU________AGUGU...UAG-5'\n_____________\|________\|\n_____________28_______12\n	3 -- 9	174 -- 180	-7.89877 kcal/mol	1.882 kcal/mol	0.273058 kcal/mol	181 196@LB@ \| \|@LB@ 5'-U AUGGU...CGC-3'@LB@ AUAUUCAG@LB@ \|\|\|:\|\|\|\|@LB@ UAUGAGUC@LB@3'-UUU...GUGGU AGUGU...UAG-5'@LB@ \| \|@LB@ 28 12@LB@@LB@@LB@Energy -13.07 kcal/mol@LB@Hybridization Energy -7.89877 kcal/mol@LB@Unfolding Energy - mRNA 1.882 kcal/mol@LB@Unfolding Energy - sRNA 0.273058 kcal/mol@LB@@LB@Position - mRNA 182 -- 195@LB@Position - sRNA 13 -- 27@LB@Position Seed - mRNA 3 -- 9@LB@Position Seed - sRNA 174 -- 180@LB@
87	0.009479	0.3575	b1192	ldcA	-9.25	0.375459	184 -- 216	125 -- 154	murein tetrapeptide carboxypeptidase; LD-carboxypeptidase A		_____________183_______________217\n_____________\|_________________\|\n5'-UGC...AGCAC__CG_____________UCCAG...UCA-3'\n______________GC__CGCUG_CGUGGUA\n______________:\|__\|\|\|\|\|_\|\|:\|\|\|\|\n______________UG__GCGAC_GCGCCAU\n3'-UUU...CGUGU__AA_____A_______UUUAU...UAG-5'\n_____________\|_________________\|\n_____________155_______________124\n	261 -- 267	48 -- 54	-20.6657 kcal/mol	8.36057 kcal/mol	6.14531 kcal/mol	183 217@LB@ \| \|@LB@5'-UGC...AGCAC CG UCCAG...UCA-3'@LB@ GC CGCUG CGUGGUA@LB@ :\| \|\|\|\|\| \|\|:\|\|\|\|@LB@ UG GCGAC GCGCCAU@LB@3'-UUU...CGUGU AA A UUUAU...UAG-5'@LB@ \| \|@LB@ 155 124@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -20.6657 kcal/mol@LB@Unfolding Energy - mRNA 8.36057 kcal/mol@LB@Unfolding Energy - sRNA 6.14531 kcal/mol@LB@@LB@Position - mRNA 184 -- 216@LB@Position - sRNA 125 -- 154@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 48 -- 54@LB@
27	0.002233	0.2633	b3525	yhjH	-10.03	0.271118	185 -- 216	151 -- 171	cyclic-di-GMP phosphodiesterase FlhDC-regulated		_____________184_______________________________217\n_____________\|_________________________________\|\n5'-UUA...UUUAA__A___G_____CUU_____AUA__________UCCAG...CCU-3'\n______________AC_CAG__ACAU___UGAUG___AGGCAGGUUA\n______________\|\|_\|\|\|__\|\|\|:___\|\|\|\|\|___\|\|\|\|\|:\|\|:\|\n______________UG_GUC__UGUG___ACUAC___UCCGUUCAGU\n3'-UUU...GGUUA__A___AG____U_______G____________UGAAA...UAG-5'\n_____________\|_________________________________\|\n_____________172_______________________________150\n	209 -- 215	152 -- 158	-24.6278 kcal/mol	4.97701 kcal/mol	8.14531 kcal/mol	184 217@LB@ \| \|@LB@5'-UUA...UUUAA A G CUU AUA UCCAG...CCU-3'@LB@ AC CAG ACAU UGAUG AGGCAGGUUA@LB@ \|\| \|\|\| \|\|\|: \|\|\|\|\| \|\|\|\|\|:\|\|:\|@LB@ UG GUC UGUG ACUAC UCCGUUCAGU@LB@3'-UUU...GGUUA A AG U G UGAAA...UAG-5'@LB@ \| \|@LB@ 172 150@LB@@LB@@LB@Energy -10.03 kcal/mol@LB@Hybridization Energy -24.6278 kcal/mol@LB@Unfolding Energy - mRNA 4.97701 kcal/mol@LB@Unfolding Energy - sRNA 8.14531 kcal/mol@LB@@LB@Position - mRNA 185 -- 216@LB@Position - sRNA 151 -- 171@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 152 -- 158@LB@
130	0.0142	0.3575	b0885	aat	-14.04	0.042507	189 -- 220	112 -- 144	leucyl/phenylalanyl-tRNA-protein transferase		_____________188_______________________________221\n_____________\|_________________________________\|\n5'-CGU...UUUUG________________CU_______________UCGCC...UUA-3'\n______________CGGUCAUGC_____GC__GGU___UCAGCUUUC\n______________\|:\|\|\|\|::\|_____\|\|__\|\|:___\|\|\|:\|\|\|\|\|\n______________GUCAGUGUG_____CG__CCG___AGUUGAAAG\n3'-UUU...UAUGA_________UACUA__U____UUC_________UCUUA...UAG-5'\n_____________\|_________________________________\|\n_____________145_______________________________111\n	214 -- 220	145 -- 151	-24.916 kcal/mol	8.31603 kcal/mol	8.21863 kcal/mol	188 221@LB@ \| \|@LB@5'-CGU...UUUUG CU UCGCC...UUA-3'@LB@ CGGUCAUGC GC GGU UCAGCUUUC@LB@ \|:\|\|\|\|::\| \|\| \|\|: \|\|\|:\|\|\|\|\|@LB@ GUCAGUGUG CG CCG AGUUGAAAG@LB@3'-UUU...UAUGA UACUA U UUC UCUUA...UAG-5'@LB@ \| \|@LB@ 145 111@LB@@LB@@LB@Energy -14.04 kcal/mol@LB@Hybridization Energy -24.916 kcal/mol@LB@Unfolding Energy - mRNA 8.31603 kcal/mol@LB@Unfolding Energy - sRNA 8.21863 kcal/mol@LB@@LB@Position - mRNA 189 -- 220@LB@Position - sRNA 112 -- 144@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 145 -- 151@LB@
182	0.02094	0.3833	b0248	yafX	-12.67	0.081205	189 -- 235	52 -- 92	CP4-6 prophage; uncharacterized protein	b2643	_____________188______________________236\n_____________\|________________________\|\n5'-CCG...ACACA___G_________C____ACC___UAACC...GGC-3'\n______________GAC_CAGCACGAC_UCGC___CGC\n______________:\|\|_\|\|\|\|\|\|:\|\|_\|\|\|\|___\|\|\|\n______________UUG_GUCGUGUUG_AGCG___GCG\n3'-UUU...UUGCG_____________A____ACA___CCAUU...UAG-5'\n_____________\|________________________\|\n_____________93_______________________51\n	218 -- 224	63 -- 69	-27.2596 kcal/mol	3.0161 kcal/mol	15.5954 kcal/mol	188 236@LB@ \| \|@LB@5'-CCG...ACACA G C ACC UAACC...GGC-3'@LB@ GAC CAGCACGAC UCGC CGC@LB@ :\|\| \|\|\|\|\|\|:\|\| \|\|\|\| \|\|\|@LB@ UUG GUCGUGUUG AGCG GCG@LB@3'-UUU...UUGCG A ACA CCAUU...UAG-5'@LB@ \| \|@LB@ 93 51@LB@@LB@@LB@Energy -12.67 kcal/mol@LB@Hybridization Energy -27.2596 kcal/mol@LB@Unfolding Energy - mRNA 3.0161 kcal/mol@LB@Unfolding Energy - sRNA 15.5954 kcal/mol@LB@@LB@Position - mRNA 189 -- 235@LB@Position - sRNA 52 -- 92@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 63 -- 69@LB@
121	0.01323	0.3575	b3429	glgA	-14.56	0.033318	190 -- 240	123 -- 176	glycogen synthase		_____________189__________________241\n_____________\|____________________\|\n5'-GUA...AUGCA__________GU________AGAUG...ACG-3'\n______________GGUUUUACAU__AUGUUCAG\n______________\|:\|\|\|\|\|\|\|:__\|\|::\|\|\|\|\n______________CUAAAAUGUG__UAUGAGUC\n3'-UUU...GCCCA__________GU________AGUGU...UAG-5'\n_____________\|____________________\|\n_____________177__________________122\n	219 -- 225	174 -- 180	-15.9439 kcal/mol	3.46677 kcal/mol	4.94566 kcal/mol	189 241@LB@ \| \|@LB@5'-GUA...AUGCA GU AGAUG...ACG-3'@LB@ GGUUUUACAU AUGUUCAG@LB@ \|:\|\|\|\|\|\|\|: \|\|::\|\|\|\|@LB@ CUAAAAUGUG UAUGAGUC@LB@3'-UUU...GCCCA GU AGUGU...UAG-5'@LB@ \| \|@LB@ 177 122@LB@@LB@@LB@Energy -14.56 kcal/mol@LB@Hybridization Energy -15.9439 kcal/mol@LB@Unfolding Energy - mRNA 3.46677 kcal/mol@LB@Unfolding Energy - sRNA 4.94566 kcal/mol@LB@@LB@Position - mRNA 190 -- 240@LB@Position - sRNA 123 -- 176@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 174 -- 180@LB@
102	0.01106	0.3575	b0647	ybeT	-15.01	0.026876	192 -- 264	115 -- 176	Sel1 family TPR-like repeat protein		_____________191___________265\n_____________\|_____________\|\n5'-AUA...CGAAG__U__________AUAAA...UGG-3'\n______________CA_UCACACAUGA\n______________\|\|_\|\|\|\|\|\|\|\|\|\|\n______________GU_AGUGUGUACU\n3'-UUU...UAUGA__C__________ACGUC...UAG-5'\n_____________\|_____________\|\n_____________177___________114\n	198 -- 204	164 -- 170	-15.9732 kcal/mol	2.87622 kcal/mol	4.17773 kcal/mol	191 265@LB@ \| \|@LB@5'-AUA...CGAAG U AUAAA...UGG-3'@LB@ CA UCACACAUGA@LB@ \|\| \|\|\|\|\|\|\|\|\|\|@LB@ GU AGUGUGUACU@LB@3'-UUU...UAUGA C ACGUC...UAG-5'@LB@ \| \|@LB@ 177 114@LB@@LB@@LB@Energy -15.01 kcal/mol@LB@Hybridization Energy -15.9732 kcal/mol@LB@Unfolding Energy - mRNA 2.87622 kcal/mol@LB@Unfolding Energy - sRNA 4.17773 kcal/mol@LB@@LB@Position - mRNA 192 -- 264@LB@Position - sRNA 115 -- 176@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 164 -- 170@LB@
88	0.009956	0.3575	b2672	ygaM	-12.38	0.093122	193 -- 231	56 -- 92	putative membrane-anchored DUF883 family ribosome-binding protein		_____________192______232\n_____________\|________\|\n5'-AAC...UGAAC________AGAAA...AGU-3'\n______________CUCAGUUA\n______________\|\|\|\|\|\|:\|\n______________GAGUCAGU\n3'-UUU...GUUAU________GUGUA...UAG-5'\n_____________\|________\|\n_____________93_______55\n	142 -- 148	171 -- 177	-10.1878 kcal/mol	1.87036 kcal/mol	0.207782 kcal/mol	192 232@LB@ \| \|@LB@5'-AAC...UGAAC AGAAA...AGU-3'@LB@ CUCAGUUA@LB@ \|\|\|\|\|\|:\|@LB@ GAGUCAGU@LB@3'-UUU...GUUAU GUGUA...UAG-5'@LB@ \| \|@LB@ 93 55@LB@@LB@@LB@Energy -12.38 kcal/mol@LB@Hybridization Energy -10.1878 kcal/mol@LB@Unfolding Energy - mRNA 1.87036 kcal/mol@LB@Unfolding Energy - sRNA 0.207782 kcal/mol@LB@@LB@Position - mRNA 193 -- 231@LB@Position - sRNA 56 -- 92@LB@Position Seed - mRNA 142 -- 148@LB@Position Seed - sRNA 171 -- 177@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