Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
11	0.0003708	0.1087	b4201	priB	-14.90	0.029310	176 -- 193	6 -- 26	primosomal protein N		_____________175___________________194\n_____________\|_____________________\|\n5'-AGG...GAAGC__________U__________AUUUC...AUC-3'\n______________UGGGGAU_UC___GAAGAGUA\n______________\|\|\|\|\|\|:_\|\|___\|\|\|:\|\|:\|\n______________ACCCCUG_AG___CUUUUCGU\n3'-UUU...GUUUU_______U__UUU________CACCG-5'\n_____________\|_____________________\|\n_____________27____________________5\n	187 -- 193	6 -- 12	-19.0189 kcal/mol	3.41067 kcal/mol	0.706421 kcal/mol	175 194@LB@ \| \|@LB@5'-AGG...GAAGC U AUUUC...AUC-3'@LB@ UGGGGAU UC GAAGAGUA@LB@ \|\|\|\|\|\|: \|\| \|\|\|:\|\|:\|@LB@ ACCCCUG AG CUUUUCGU@LB@3'-UUU...GUUUU U UUU CACCG-5'@LB@ \| \|@LB@ 27 5@LB@@LB@@LB@Energy -14.90 kcal/mol@LB@Hybridization Energy -19.0189 kcal/mol@LB@Unfolding Energy - mRNA 3.41067 kcal/mol@LB@Unfolding Energy - sRNA 0.706421 kcal/mol@LB@@LB@Position - mRNA 176 -- 193@LB@Position - sRNA 6 -- 26@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 6 -- 12@LB@
12	0.0004023	0.1087	b3176	glmM	-16.74	0.009770	131 -- 153	1 -- 22	phosphoglucosamine mutase		_____________130_____________________154\n_____________\|_______________________\|\n5'-GUU...UUCAU_____________CC____AA__GAUGC...CGG-3'\n______________GACGUCAAAGAAA__GUAG__GC\n______________\|\|\|:\|\|\|\|\|\|\|\|\|__\|:\|\|__\|\|\n______________CUGUAGUUUCUUU__CGUC__CG\n3'-UUU...UACCC_____________U_____AC__-5'\n_____________\|______________________\|\n_____________23_____________________1\n	137 -- 143	10 -- 16	-21.6768 kcal/mol	3.39473 kcal/mol	1.54023 kcal/mol	130 154@LB@ \| \|@LB@5'-GUU...UUCAU CC AA GAUGC...CGG-3'@LB@ GACGUCAAAGAAA GUAG GC@LB@ \|\|\|:\|\|\|\|\|\|\|\|\| \|:\|\| \|\|@LB@ CUGUAGUUUCUUU CGUC CG@LB@3'-UUU...UACCC U AC -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -16.74 kcal/mol@LB@Hybridization Energy -21.6768 kcal/mol@LB@Unfolding Energy - mRNA 3.39473 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 131 -- 153@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 137 -- 143@LB@Position Seed - sRNA 10 -- 16@LB@
13	0.0004028	0.1087	b1107	nagZ	-16.35	0.012500	184 -- 201	3 -- 21	beta N-acetyl-glucosaminidase		_____________183_________________202\n_____________\|___________________\|\n5'-AUU...AUAAA___AU______________UGGGU...CGC-3'\n______________ACA___AAGGAGAGCAGUG\n______________\|\|\|___\|\|\|:\|:\|\|\|\|\|\|\|\n______________UGU___UUCUUUUCGUCAC\n3'-UUU...ACCCC___AGU_____________CG-5'\n_____________\|___________________\|\n_____________22__________________2\n	195 -- 201	3 -- 9	-19.0842 kcal/mol	1.22154 kcal/mol	1.5107 kcal/mol	183 202@LB@ \| \|@LB@5'-AUU...AUAAA AU UGGGU...CGC-3'@LB@ ACA AAGGAGAGCAGUG@LB@ \|\|\| \|\|\|:\|:\|\|\|\|\|\|\|@LB@ UGU UUCUUUUCGUCAC@LB@3'-UUU...ACCCC AGU CG-5'@LB@ \| \|@LB@ 22 2@LB@@LB@@LB@Energy -16.35 kcal/mol@LB@Hybridization Energy -19.0842 kcal/mol@LB@Unfolding Energy - mRNA 1.22154 kcal/mol@LB@Unfolding Energy - sRNA 1.5107 kcal/mol@LB@@LB@Position - mRNA 184 -- 201@LB@Position - sRNA 3 -- 21@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 3 -- 9@LB@
14	0.0006392	0.1243	b3745	viaA	-13.90	0.050132	246 -- 264	10 -- 25	stimulator of RavA ATPase activity; von Willebrand factor domain protein		_____________245_________________265\n_____________\|___________________\|\n5'-ACG...GCGAA_A_____UG__________UGAUC...CGG-3'\n______________G_GGGAU__AUCGAAGAGA\n______________\|_\|\|\|\|:__\|\|\|:\|\|\|\|:\|\n______________C_CCCUG__UAGUUUCUUU\n3'-UUU...UUUUA___________________UCGUC...CCG-5'\n_____________\|___________________\|\n_____________26__________________9\n	258 -- 264	10 -- 16	-16.9183 kcal/mol	2.35086 kcal/mol	0.670388 kcal/mol	245 265@LB@ \| \|@LB@5'-ACG...GCGAA A UG UGAUC...CGG-3'@LB@ G GGGAU AUCGAAGAGA@LB@ \| \|\|\|\|: \|\|\|:\|\|\|\|:\|@LB@ C CCCUG UAGUUUCUUU@LB@3'-UUU...UUUUA UCGUC...CCG-5'@LB@ \| \|@LB@ 26 9@LB@@LB@@LB@Energy -13.90 kcal/mol@LB@Hybridization Energy -16.9183 kcal/mol@LB@Unfolding Energy - mRNA 2.35086 kcal/mol@LB@Unfolding Energy - sRNA 0.670388 kcal/mol@LB@@LB@Position - mRNA 246 -- 264@LB@Position - sRNA 10 -- 25@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 10 -- 16@LB@
15	0.0006403	0.1243	b0178	skp	-17.37	0.006465	90 -- 106	1 -- 17	periplasmic chaperone		_____________89________________107\n_____________\|_________________\|\n5'-CUC...CUCCA________U________AGUGU...UCC-3'\n______________CAAAGGAA_GUAGUGGU\n______________\|\|\|\|\|:\|\|_\|:\|\|\|\|\|:\n______________GUUUCUUU_CGUCACCG\n3'-UUU...CUGUA________U________-5'\n_____________\|________________\|\n_____________18_______________1\n	100 -- 106	1 -- 7	-21.6829 kcal/mol	2.87621 kcal/mol	1.43853 kcal/mol	89 107@LB@ \| \|@LB@5'-CUC...CUCCA U AGUGU...UCC-3'@LB@ CAAAGGAA GUAGUGGU@LB@ \|\|\|\|\|:\|\| \|:\|\|\|\|\|:@LB@ GUUUCUUU CGUCACCG@LB@3'-UUU...CUGUA U -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -17.37 kcal/mol@LB@Hybridization Energy -21.6829 kcal/mol@LB@Unfolding Energy - mRNA 2.87621 kcal/mol@LB@Unfolding Energy - sRNA 1.43853 kcal/mol@LB@@LB@Position - mRNA 90 -- 106@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 1 -- 7@LB@
16	0.0006527	0.1243	b2563	acpS	-16.60	0.010715	145 -- 164	1 -- 23	holo-[acyl-carrier-protein] synthase 1		_____________144_____________________165\n_____________\|_______________________\|\n5'-GCC...UGACC______G_____U__________AGAAA...GCG-3'\n______________GGAC_U_AAAGA___GCGGUGGC\n______________\|\|\|\|_\|_\|\|\|\|\|___\|\|:\|\|\|\|\|\n______________CCUG_A_UUUCU___CGUCACCG\n3'-UUU...UUACC____U_G_____UUU________-5'\n_____________\|______________________\|\n_____________24_____________________1\n	158 -- 164	1 -- 7	-25.7246 kcal/mol	7.54829 kcal/mol	1.57928 kcal/mol	144 165@LB@ \| \|@LB@5'-GCC...UGACC G U AGAAA...GCG-3'@LB@ GGAC U AAAGA GCGGUGGC@LB@ \|\|\|\| \| \|\|\|\|\| \|\|:\|\|\|\|\|@LB@ CCUG A UUUCU CGUCACCG@LB@3'-UUU...UUACC U G UUU -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -16.60 kcal/mol@LB@Hybridization Energy -25.7246 kcal/mol@LB@Unfolding Energy - mRNA 7.54829 kcal/mol@LB@Unfolding Energy - sRNA 1.57928 kcal/mol@LB@@LB@Position - mRNA 145 -- 164@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 1 -- 7@LB@
17	0.0006839	0.1243	b1247	oppF	-10.96	0.191014	264 -- 288	1 -- 22	oligopeptide ABC transporter ATPase		_____________263________________________289\n_____________\|__________________________\|\n5'-GCG...ACUUU__A________U____AAAC______UCUGG...CGC-3'\n______________GA_AUCAAAGA__GGC____AGUGGU\n______________\|\|_\|\|\|\|\|\|\|\|__:\|\|____\|\|\|\|\|:\n______________CU_UAGUUUCU__UCG____UCACCG\n3'-UUU...UACCC__G________UU_____________-5'\n_____________\|_________________________\|\n_____________23________________________1\n	268 -- 274	12 -- 18	-19.2479 kcal/mol	6.74487 kcal/mol	1.54023 kcal/mol	263 289@LB@ \| \|@LB@5'-GCG...ACUUU A U AAAC UCUGG...CGC-3'@LB@ GA AUCAAAGA GGC AGUGGU@LB@ \|\| \|\|\|\|\|\|\|\| :\|\| \|\|\|\|\|:@LB@ CU UAGUUUCU UCG UCACCG@LB@3'-UUU...UACCC G UU -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -10.96 kcal/mol@LB@Hybridization Energy -19.2479 kcal/mol@LB@Unfolding Energy - mRNA 6.74487 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 264 -- 288@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 12 -- 18@LB@
18	0.0007186	0.1243	b3657	yicJ	-19.60	0.001218	184 -- 200	5 -- 21	putative transporter		_____________183_______________201\n_____________\|_________________\|\n5'-CAG...CUAUA_________________AUGAA...UGU-3'\n______________GCAUCAAGGAAAAGCAG\n______________:\|\|\|\|\|\|:\|\|\|\|\|\|\|\|\|\n______________UGUAGUUUCUUUUCGUC\n3'-UUU...ACCCC_________________ACCG-5'\n_____________\|_________________\|\n_____________22________________4\n	194 -- 200	5 -- 11	-25.6417 kcal/mol	4.53845 kcal/mol	1.5073 kcal/mol	183 201@LB@ \| \|@LB@5'-CAG...CUAUA AUGAA...UGU-3'@LB@ GCAUCAAGGAAAAGCAG@LB@ :\|\|\|\|\|\|:\|\|\|\|\|\|\|\|\|@LB@ UGUAGUUUCUUUUCGUC@LB@3'-UUU...ACCCC ACCG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -19.60 kcal/mol@LB@Hybridization Energy -25.6417 kcal/mol@LB@Unfolding Energy - mRNA 4.53845 kcal/mol@LB@Unfolding Energy - sRNA 1.5073 kcal/mol@LB@@LB@Position - mRNA 184 -- 200@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 5 -- 11@LB@
19	0.000738	0.1243	b1508	hipB	-18.00	0.004180	266 -- 295	1 -- 32	antitoxin of HipAB toxin-antitoxin system	b1299 b1434	_____________265________________________________296\n_____________\|__________________________________\|\n5'-AUG...CGCCA_________CU___________C___________GAAAA-3'\n______________GCAAAAUGG__GGACG_CAGAG__GAGC__UGGC\n______________:\|\|\|\|\|\|\|\|__\|\|\|\|:_\|\|:\|\|__:\|\|\|__\|\|\|\|\n______________UGUUUUACC__CCUGU_GUUUC__UUCG__ACCG\n3'-UUU...CGAGG________________A_____UU____UC____-5'\n_____________\|_________________________________\|\n_____________33________________________________1\n	268 -- 274	24 -- 30	-30.0826 kcal/mol	9.54799 kcal/mol	2.53929 kcal/mol	265 296@LB@ \| \|@LB@5'-AUG...CGCCA CU C GAAAA-3'@LB@ GCAAAAUGG GGACG CAGAG GAGC UGGC@LB@ :\|\|\|\|\|\|\|\| \|\|\|\|: \|\|:\|\| :\|\|\| \|\|\|\|@LB@ UGUUUUACC CCUGU GUUUC UUCG ACCG@LB@3'-UUU...CGAGG A UU UC -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -18.00 kcal/mol@LB@Hybridization Energy -30.0826 kcal/mol@LB@Unfolding Energy - mRNA 9.54799 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 266 -- 295@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 24 -- 30@LB@
20	0.0007622	0.1243	b1507	hipA	-19.17	0.001718	1 -- 29	1 -- 31	inactivating GltX kinase facilitating persister formation; toxin of HipAB TA pair; autokinase		______________1________________________________30\n______________\|________________________________\|\n___________5'-________CU___________C___________GAAAA...UAG-3'\n______________CAAAAUGG__GGACG_CAGAG__GAGC__UGGC\n______________\|\|\|\|\|\|\|\|__\|\|\|\|:_\|\|:\|\|__:\|\|\|__\|\|\|\|\n______________GUUUUACC__CCUGU_GUUUC__UUCG__ACCG\n3'-UUU...GAGGU_______________A_____UU____UC____-5'\n_____________\|________________________________\|\n_____________32_______________________________1\n	2 -- 8	24 -- 30	-30.0086 kcal/mol	8.29611 kcal/mol	2.53929 kcal/mol	1 30@LB@ \| \|@LB@ 5'- CU C GAAAA...UAG-3'@LB@ CAAAAUGG GGACG CAGAG GAGC UGGC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|: \|\|:\|\| :\|\|\| \|\|\|\|@LB@ GUUUUACC CCUGU GUUUC UUCG ACCG@LB@3'-UUU...GAGGU A UU UC -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -19.17 kcal/mol@LB@Hybridization Energy -30.0086 kcal/mol@LB@Unfolding Energy - mRNA 8.29611 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 1 -- 29@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 2 -- 8@LB@Position Seed - sRNA 24 -- 30@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