Input and runtime details for job 2727377 (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 2727377 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:09 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:28 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:18:35 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:18:43 CET 2018
	Job Completed		@ Fri Feb 16 20:19:11 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=2727377&toolName=CopraRNA ( 30 days expiry )

Description of the job

RyhB

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
43	0.003552	0.2776	b3453	ugpB	-15.55	0.022327	231 -- 272	40 -- 85	sn-glycerol-3-phosphate ABC transporter periplasmic binding protein	_____________230______________________________________________273\n_____________\|________________________________________________\|\n5'-UUC...CAGCA___________A_____GU_______G_____U___CA__________ACGAC...UGG-3'\n______________CUGGCGCUCGG_CUGGC____UAAUG__GGAA_GCA_____GGCAGUG\n______________\|::\|\|:\|:\|\|\|_\|\|\|\|\|____\|\|\|\|:__\|\|\|\|_\|\|\|_____:\|\|\|:\|\|\n______________GGUCGUGGGCC_GACCG____AUUAU__CCUU_CGU_____UCGUUAC\n______3'-UUUUC_________________AUUC_____GA________UACAC_______AGCAC...GCG-5'\n_____________\|________________________________________________\|\n_____________86_______________________________________________39\n	266 -- 272	40 -- 46	-44.9281 kcal/mol	14.4718 kcal/mol	14.9103 kcal/mol	230 273@LB@ \| \|@LB@5'-UUC...CAGCA A GU G U CA ACGAC...UGG-3'@LB@ CUGGCGCUCGG CUGGC UAAUG GGAA GCA GGCAGUG@LB@ \|::\|\|:\|:\|\|\| \|\|\|\|\| \|\|\|\|: \|\|\|\| \|\|\| :\|\|\|:\|\|@LB@ GGUCGUGGGCC GACCG AUUAU CCUU CGU UCGUUAC@LB@ 3'-UUUUC AUUC GA UACAC AGCAC...GCG-5'@LB@ \| \|@LB@ 86 39@LB@@LB@@LB@Energy -15.55 kcal/mol@LB@Hybridization Energy -44.9281 kcal/mol@LB@Unfolding Energy - mRNA 14.4718 kcal/mol@LB@Unfolding Energy - sRNA 14.9103 kcal/mol@LB@@LB@Position - mRNA 231 -- 272@LB@Position - sRNA 40 -- 85@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 40 -- 46@LB@
45	0.00394	0.2905	b4551	yheV	-11.41	0.111890	172 -- 193	40 -- 61	DUF2387 family putative metal-binding protein	_____________171____________________194\n_____________\|______________________\|\n5'-AUC...GGACG_______UG___U_______A_GGUAA...UUG-3'\n______________GCUGGGA__AAU_UGAGUAG_G\n______________:\|\|\|\|:\|__\|\|\|_\|\|\|\|:\|:_\|\n______________UGACCUU__UUA_ACUCGUU_C\n3'-UUU...CAUUA_______CG___C_______A_AGCAC...GCG-5'\n_____________\|______________________\|\n_____________62_____________________39\n	185 -- 191	42 -- 48	-20.0831 kcal/mol	5.37544 kcal/mol	3.30075 kcal/mol	171 194@LB@ \| \|@LB@5'-AUC...GGACG UG U A GGUAA...UUG-3'@LB@ GCUGGGA AAU UGAGUAG G@LB@ :\|\|\|\|:\| \|\|\| \|\|\|\|:\|: \|@LB@ UGACCUU UUA ACUCGUU C@LB@3'-UUU...CAUUA CG C A AGCAC...GCG-5'@LB@ \| \|@LB@ 62 39@LB@@LB@@LB@Energy -11.41 kcal/mol@LB@Hybridization Energy -20.0831 kcal/mol@LB@Unfolding Energy - mRNA 5.37544 kcal/mol@LB@Unfolding Energy - sRNA 3.30075 kcal/mol@LB@@LB@Position - mRNA 172 -- 193@LB@Position - sRNA 40 -- 61@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 42 -- 48@LB@
50	0.004678	0.2905	b0906	ycaP	-14.80	0.029952	1 -- 24	40 -- 67	UPF0702 family putative inner membrane protein	______________1____________________________25\n______________\|____________________________\|\n___________5'-___UUU_______________________GAAUC...UCU-3'\n______________AGU___UGCUGGAAGC_____GAGCGAUG\n______________\|\|\|___\|:\|\|\|\|\|\|\|\|_____\|\|\|\|:\|\|\|\n______________UCA___AUGACCUUCG_____CUCGUUAC\n3'-UUU...CCGAU___UU___________UUACA________AGCAC...GCG-5'\n_____________\|_____________________________\|\n_____________68____________________________39\n	18 -- 24	40 -- 46	-27.5061 kcal/mol	9.39751 kcal/mol	3.30504 kcal/mol	1 25@LB@ \| \|@LB@ 5'- UUU GAAUC...UCU-3'@LB@ AGU UGCUGGAAGC GAGCGAUG@LB@ \|\|\| \|:\|\|\|\|\|\|\|\| \|\|\|\|:\|\|\|@LB@ UCA AUGACCUUCG CUCGUUAC@LB@3'-UUU...CCGAU UU UUACA AGCAC...GCG-5'@LB@ \| \|@LB@ 68 39@LB@@LB@@LB@Energy -14.80 kcal/mol@LB@Hybridization Energy -27.5061 kcal/mol@LB@Unfolding Energy - mRNA 9.39751 kcal/mol@LB@Unfolding Energy - sRNA 3.30504 kcal/mol@LB@@LB@Position - mRNA 1 -- 24@LB@Position - sRNA 40 -- 67@LB@Position Seed - mRNA 18 -- 24@LB@Position Seed - sRNA 40 -- 46@LB@
71	0.00621	0.2939	b0178	skp	-11.69	0.100677	99 -- 118	40 -- 66	periplasmic chaperone	_____________98__________________________119\n_____________\|___________________________\|\n5'-CUC...GGAAU___________________________ACUUU...UCC-3'\n______________GUAGU______GGUAGUGU_AGCGAUG\n______________\|\|\|:\|______:\|:\|:\|\|\|_\|\|\|:\|\|\|\n______________CAUUA______UCGUUACA_UCGUUAC\n3'-UUU...CGAUU_____UGACCU________C_______AGCAC...GCG-5'\n_____________\|___________________________\|\n_____________67__________________________39\n	112 -- 118	40 -- 46	-18.9809 kcal/mol	3.99027 kcal/mol	3.30497 kcal/mol	98 119@LB@ \| \|@LB@5'-CUC...GGAAU ACUUU...UCC-3'@LB@ GUAGU GGUAGUGU AGCGAUG@LB@ \|\|\|:\| :\|:\|:\|\|\| \|\|\|:\|\|\|@LB@ CAUUA UCGUUACA UCGUUAC@LB@3'-UUU...CGAUU UGACCU C AGCAC...GCG-5'@LB@ \| \|@LB@ 67 39@LB@@LB@@LB@Energy -11.69 kcal/mol@LB@Hybridization Energy -18.9809 kcal/mol@LB@Unfolding Energy - mRNA 3.99027 kcal/mol@LB@Unfolding Energy - sRNA 3.30497 kcal/mol@LB@@LB@Position - mRNA 99 -- 118@LB@Position - sRNA 40 -- 66@LB@Position Seed - mRNA 112 -- 118@LB@Position Seed - sRNA 40 -- 46@LB@
87	0.008915	0.3393	b2530	iscS	-12.30	0.079567	175 -- 203	40 -- 68	cysteine desulfurase (tRNA sulfurtransferase) PLP-dependent	_____________174___________________________204\n_____________\|_____________________________\|\n5'-AAG...GCAUU________UAC_____UUAUA________AAAUU...UUG-3'\n______________GAGUGAUG___GGAGU_____GAGCAAUG\n______________:\|\|\|:\|\|:___\|:\|\|:_____\|\|\|\|\|\|\|\|\n______________UUCAUUAU___CUUCG_____CUCGUUAC\n3'-UUU...ACCGA________GAC_____UUACA________AGCAC...GCG-5'\n_____________\|_____________________________\|\n_____________69____________________________39\n	197 -- 203	40 -- 46	-22.6486 kcal/mol	7.04226 kcal/mol	3.30507 kcal/mol	174 204@LB@ \| \|@LB@5'-AAG...GCAUU UAC UUAUA AAAUU...UUG-3'@LB@ GAGUGAUG GGAGU GAGCAAUG@LB@ :\|\|\|:\|\|: \|:\|\|: \|\|\|\|\|\|\|\|@LB@ UUCAUUAU CUUCG CUCGUUAC@LB@3'-UUU...ACCGA GAC UUACA AGCAC...GCG-5'@LB@ \| \|@LB@ 69 39@LB@@LB@@LB@Energy -12.30 kcal/mol@LB@Hybridization Energy -22.6486 kcal/mol@LB@Unfolding Energy - mRNA 7.04226 kcal/mol@LB@Unfolding Energy - sRNA 3.30507 kcal/mol@LB@@LB@Position - mRNA 175 -- 203@LB@Position - sRNA 40 -- 68@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 40 -- 46@LB@
97	0.0101	0.3393	b0192	nlpE	-13.07	0.059097	192 -- 230	40 -- 68	lipoprotein involved with copper homeostasis and adhesion	_____________191_____________________________________231\n_____________\|_______________________________________\|\n5'-UCA...AAAAG___GA___GA___UGAAAA_______A____CA______GCUGU...CGC-3'\n______________AAG__AUG__UGG______AAGCGAU_GUGA__GCGAUG\n______________\|\|\|__\|\|:__\|\|\|______\|\|\|\|:\|\|_\|\|\|\|__\|\|:\|\|\|\n______________UUC__UAU__ACC______UUCGUUA_CACU__CGUUAC\n3'-UUU...ACCGA___AU___G______________________________AGCAC...GCG-5'\n_____________\|_______________________________________\|\n_____________69______________________________________39\n	211 -- 217	50 -- 56	-20.8621 kcal/mol	4.48665 kcal/mol	3.30507 kcal/mol	191 231@LB@ \| \|@LB@5'-UCA...AAAAG GA GA UGAAAA A CA GCUGU...CGC-3'@LB@ AAG AUG UGG AAGCGAU GUGA GCGAUG@LB@ \|\|\| \|\|: \|\|\| \|\|\|\|:\|\| \|\|\|\| \|\|:\|\|\|@LB@ UUC UAU ACC UUCGUUA CACU CGUUAC@LB@3'-UUU...ACCGA AU G AGCAC...GCG-5'@LB@ \| \|@LB@ 69 39@LB@@LB@@LB@Energy -13.07 kcal/mol@LB@Hybridization Energy -20.8621 kcal/mol@LB@Unfolding Energy - mRNA 4.48665 kcal/mol@LB@Unfolding Energy - sRNA 3.30507 kcal/mol@LB@@LB@Position - mRNA 192 -- 230@LB@Position - sRNA 40 -- 68@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 50 -- 56@LB@
114	0.01202	0.3513	b4348	hsdS	-14.85	0.029459	128 -- 148	40 -- 66	specificity determinant for hsdM and hsdR	_____________127_________________________149\n_____________\|___________________________\|\n5'-CUG...GAUGC___________________________AGGCC...UAA-3'\n______________GUGA_ACUGGGGGC_____GAGCGAUG\n______________\|\|:\|_\|\|\|\|\|::\|\|_____\|\|\|\|:\|\|\|\n______________CAUU_UGACCUUCG_____CUCGUUAC\n3'-UUU...CGAUU____A_________UUACA________AGCAC...GCG-5'\n_____________\|___________________________\|\n_____________67__________________________39\n	142 -- 148	40 -- 46	-25.5951 kcal/mol	7.44461 kcal/mol	3.30497 kcal/mol	127 149@LB@ \| \|@LB@5'-CUG...GAUGC AGGCC...UAA-3'@LB@ GUGA ACUGGGGGC GAGCGAUG@LB@ \|\|:\| \|\|\|\|\|::\|\| \|\|\|\|:\|\|\|@LB@ CAUU UGACCUUCG CUCGUUAC@LB@3'-UUU...CGAUU A UUACA AGCAC...GCG-5'@LB@ \| \|@LB@ 67 39@LB@@LB@@LB@Energy -14.85 kcal/mol@LB@Hybridization Energy -25.5951 kcal/mol@LB@Unfolding Energy - mRNA 7.44461 kcal/mol@LB@Unfolding Energy - sRNA 3.30497 kcal/mol@LB@@LB@Position - mRNA 128 -- 148@LB@Position - sRNA 40 -- 66@LB@Position Seed - mRNA 142 -- 148@LB@Position Seed - sRNA 40 -- 46@LB@
119	0.01272	0.3585	b4336	yjiN	-16.20	0.017192	123 -- 159	40 -- 86	zinc-type alcohol dehydrogenase-like protein	_____________122_____________________________________________160\n_____________\|_______________________________________________\|\n5'-GGU...CGUGC_________A___A___C___C____G____________________AUUUU...CCA-3'\n______________GCCAGCAUC_GGC__GC_GAG___UA_UGGAG_______GAGCAGUG\n______________\|\|\|\|\|\|\|:\|_\|\|\|__\|\|_:\|\|___\|\|_\|\|\|\|:_______\|\|\|\|\|:\|\|\n______________CGGUCGUGG_CCG__CG_UUC___AU_ACCUU_______CUCGUUAC\n_______3'-UUUU_________G___AC__A___AUU__G_____CGUUACA________AGCAC...GCG-5'\n_____________\|_______________________________________________\|\n_____________87______________________________________________39\n	153 -- 159	40 -- 46	-42.8122 kcal/mol	11.6972 kcal/mol	14.9104 kcal/mol	122 160@LB@ \| \|@LB@5'-GGU...CGUGC A A C C G AUUUU...CCA-3'@LB@ GCCAGCAUC GGC GC GAG UA UGGAG GAGCAGUG@LB@ \|\|\|\|\|\|\|:\| \|\|\| \|\| :\|\| \|\| \|\|\|\|: \|\|\|\|\|:\|\|@LB@ CGGUCGUGG CCG CG UUC AU ACCUU CUCGUUAC@LB@ 3'-UUUU G AC A AUU G CGUUACA AGCAC...GCG-5'@LB@ \| \|@LB@ 87 39@LB@@LB@@LB@Energy -16.20 kcal/mol@LB@Hybridization Energy -42.8122 kcal/mol@LB@Unfolding Energy - mRNA 11.6972 kcal/mol@LB@Unfolding Energy - sRNA 14.9104 kcal/mol@LB@@LB@Position - mRNA 123 -- 159@LB@Position - sRNA 40 -- 86@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 40 -- 46@LB@
131	0.01424	0.3651	b0058	rluA	-14.42	0.034831	43 -- 63	40 -- 60	dual specificity 23S rRNA pseudouridine(746) tRNA pseudouridine(32) synthase SAM-dependent	_____________42____________________64\n_____________\|_____________________\|\n5'-CGU...CUCGU________UC__C_U______AACCC...UGU-3'\n______________CUGGAAGC__UG_G_GCAGUG\n______________\|\|\|\|\|\|\|\|__\|\|_\|_\|\|\|:\|\|\n______________GACCUUCG__AC_C_CGUUAC\n3'-UUU...AUUAU________UU__A_U______AGCAC...GCG-5'\n_____________\|_____________________\|\n_____________61____________________39\n	44 -- 50	53 -- 59	-25.1761 kcal/mol	7.45543 kcal/mol	3.29985 kcal/mol	42 64@LB@ \| \|@LB@5'-CGU...CUCGU UC C U AACCC...UGU-3'@LB@ CUGGAAGC UG G GCAGUG@LB@ \|\|\|\|\|\|\|\| \|\| \| \|\|\|:\|\|@LB@ GACCUUCG AC C CGUUAC@LB@3'-UUU...AUUAU UU A U AGCAC...GCG-5'@LB@ \| \|@LB@ 61 39@LB@@LB@@LB@Energy -14.42 kcal/mol@LB@Hybridization Energy -25.1761 kcal/mol@LB@Unfolding Energy - mRNA 7.45543 kcal/mol@LB@Unfolding Energy - sRNA 3.29985 kcal/mol@LB@@LB@Position - mRNA 43 -- 63@LB@Position - sRNA 40 -- 60@LB@Position Seed - mRNA 44 -- 50@LB@Position Seed - sRNA 53 -- 59@LB@
149	0.01819	0.4072	b2708	srlQ	-10.57	0.153166	157 -- 203	40 -- 61	D-arabinose 5-phosphate isomerase	_____________156_____________________________________________204\n_____________\|_______________________________________________\|\n5'-UAC...CAGGC________AGAAAGGGAU______GAUCAUAACCGGAGA________AGUGA...GCG-3'\n______________GCUGGAAG__________CGAUGU_______________GAGCAAUG\n______________:\|\|\|\|\|\|\|__________\|:\|\|\|\|_______________\|\|\|\|\|\|\|\|\n______________UGACCUUC__________GUUACA_______________CUCGUUAC\n3'-UUU...CAUUA_______________________________________________AGCAC...GCG-5'\n_____________\|_______________________________________________\|\n_____________62______________________________________________39\n	197 -- 203	40 -- 46	-23.3244 kcal/mol	9.45822 kcal/mol	3.30075 kcal/mol	156 204@LB@ \| \|@LB@5'-UAC...CAGGC AGAAAGGGAU GAUCAUAACCGGAGA AGUGA...GCG-3'@LB@ GCUGGAAG CGAUGU GAGCAAUG@LB@ :\|\|\|\|\|\|\| \|:\|\|\|\| \|\|\|\|\|\|\|\|@LB@ UGACCUUC GUUACA CUCGUUAC@LB@3'-UUU...CAUUA AGCAC...GCG-5'@LB@ \| \|@LB@ 62 39@LB@@LB@@LB@Energy -10.57 kcal/mol@LB@Hybridization Energy -23.3244 kcal/mol@LB@Unfolding Energy - mRNA 9.45822 kcal/mol@LB@Unfolding Energy - sRNA 3.30075 kcal/mol@LB@@LB@Position - mRNA 157 -- 203@LB@Position - sRNA 40 -- 61@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 40 -- 46@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

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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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