Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
165	0.01953	0.3981	b0603	ybdO	-12.89	0.027143	166 -- 206	40 -- 73	putative DNA-binding transcriptional regulator	_____________165_________________________________________207\n_____________\|___________________________________________\|\n5'-UCA...GUGAA_____CA_______AAAAUAUAAC___A_______________AAUCU...CAC-3'\n______________UAUAU__UGGAAGA__________CGG__GUAGUGUA_UGGCC\n______________\|\|\|\|\|__\|\|\|\|\|:\|__________\|:\|__\|:\|:\|\|:\|_\|\|\|\|\|\n______________AUAUA__ACCUUUU__________GUC__CGUUACGU_ACCGG\n3'-UUU...GAAAA_____CA_______A____________AC________U_____GUUGU...UUG-5'\n_____________\|___________________________________________\|\n_____________74__________________________________________39\n	195 -- 201	46 -- 52	-24.6879 kcal/mol	4.92423 kcal/mol	6.86861 kcal/mol	165 207@LB@ \| \|@LB@5'-UCA...GUGAA CA AAAAUAUAAC A AAUCU...CAC-3'@LB@ UAUAU UGGAAGA CGG GUAGUGUA UGGCC@LB@ \|\|\|\|\| \|\|\|\|\|:\| \|:\| \|:\|:\|\|:\| \|\|\|\|\|@LB@ AUAUA ACCUUUU GUC CGUUACGU ACCGG@LB@3'-UUU...GAAAA CA A AC U GUUGU...UUG-5'@LB@ \| \|@LB@ 74 39@LB@@LB@@LB@Energy -12.89 kcal/mol@LB@Hybridization Energy -24.6879 kcal/mol@LB@Unfolding Energy - mRNA 4.92423 kcal/mol@LB@Unfolding Energy - sRNA 6.86861 kcal/mol@LB@@LB@Position - mRNA 166 -- 206@LB@Position - sRNA 40 -- 73@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 46 -- 52@LB@
3	3.498e-05	0.03921	b4255	rraB	-13.36	0.020838	142 -- 156	41 -- 54	protein inhibitor of RNase E	_____________141_____________157\n_____________\|_______________\|\n5'-GAG...GUGGA_______U_______GUGUG...CCA-3'\n______________GGCAAUG_CAGUGGU\n______________\|\|\|\|\|\|\|_\|\|:\|\|\|:\n______________CCGUUAC_GUUACCG\n3'-UUU...AGUCA_______________GGUUG...UUG-5'\n_____________\|_______________\|\n_____________55______________40\n	150 -- 156	41 -- 47	-21.65 kcal/mol	4.39843 kcal/mol	3.89026 kcal/mol	141 157@LB@ \| \|@LB@5'-GAG...GUGGA U GUGUG...CCA-3'@LB@ GGCAAUG CAGUGGU@LB@ \|\|\|\|\|\|\| \|\|:\|\|\|:@LB@ CCGUUAC GUUACCG@LB@3'-UUU...AGUCA GGUUG...UUG-5'@LB@ \| \|@LB@ 55 40@LB@@LB@@LB@Energy -13.36 kcal/mol@LB@Hybridization Energy -21.65 kcal/mol@LB@Unfolding Energy - mRNA 4.39843 kcal/mol@LB@Unfolding Energy - sRNA 3.89026 kcal/mol@LB@@LB@Position - mRNA 142 -- 156@LB@Position - sRNA 41 -- 54@LB@Position Seed - mRNA 150 -- 156@LB@Position Seed - sRNA 41 -- 47@LB@
32	0.002002	0.2088	b0423	thiI	-12.47	0.034301	40 -- 74	41 -- 65	tRNA s(4)U8 sulfurtransferase	_____________39_____________________________________75\n_____________\|______________________________________\|\n5'-AUG...GUAAC___C____________AUAGCAAAUAACGC________AAGGU...UUU-3'\n______________GGA___UCAG_GGCAA______________GCAAUGGU\n______________\|\|\|___\|\|\|\|_\|\|\|\|\|______________\|\|\|\|\|\|\|:\n______________CCU___AGUC_CCGUU______________CGUUACCG\n3'-UUU...UACAA___UUU____A_____A_____________________GGUUG...UUG-5'\n_____________\|______________________________________\|\n_____________66_____________________________________40\n	68 -- 74	41 -- 47	-23.8518 kcal/mol	5.56921 kcal/mol	5.80973 kcal/mol	39 75@LB@ \| \|@LB@5'-AUG...GUAAC C AUAGCAAAUAACGC AAGGU...UUU-3'@LB@ GGA UCAG GGCAA GCAAUGGU@LB@ \|\|\| \|\|\|\| \|\|\|\|\| \|\|\|\|\|\|\|:@LB@ CCU AGUC CCGUU CGUUACCG@LB@3'-UUU...UACAA UUU A A GGUUG...UUG-5'@LB@ \| \|@LB@ 66 40@LB@@LB@@LB@Energy -12.47 kcal/mol@LB@Hybridization Energy -23.8518 kcal/mol@LB@Unfolding Energy - mRNA 5.56921 kcal/mol@LB@Unfolding Energy - sRNA 5.80973 kcal/mol@LB@@LB@Position - mRNA 40 -- 74@LB@Position - sRNA 41 -- 65@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 41 -- 47@LB@
36	0.002273	0.2088	b4138	dcuA	-11.14	0.069498	259 -- 284	41 -- 65	C4-dicarboxylate antiporter	_____________258__________________________285\n_____________\|____________________________\|\n5'-AAC...AUUGG_______A___AUU___UU_________GGAUU...UGG-3'\n______________GGGGAAU_GGU___GGU__UGCA__GGC\n______________\|\|::\|\|\|_:\|\|___\|\|:__\|\|\|\|__\|\|\|\n______________CCUUUUA_UCA___CCG__ACGU__CCG\n3'-UUU...UACAA_______G_________UU____UA___GGUUG...UUG-5'\n_____________\|____________________________\|\n_____________66___________________________40\n	259 -- 265	59 -- 65	-20.3442 kcal/mol	3.39574 kcal/mol	5.80973 kcal/mol	258 285@LB@ \| \|@LB@5'-AAC...AUUGG A AUU UU GGAUU...UGG-3'@LB@ GGGGAAU GGU GGU UGCA GGC@LB@ \|\|::\|\|\| :\|\| \|\|: \|\|\|\| \|\|\|@LB@ CCUUUUA UCA CCG ACGU CCG@LB@3'-UUU...UACAA G UU UA GGUUG...UUG-5'@LB@ \| \|@LB@ 66 40@LB@@LB@@LB@Energy -11.14 kcal/mol@LB@Hybridization Energy -20.3442 kcal/mol@LB@Unfolding Energy - mRNA 3.39574 kcal/mol@LB@Unfolding Energy - sRNA 5.80973 kcal/mol@LB@@LB@Position - mRNA 259 -- 284@LB@Position - sRNA 41 -- 65@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 59 -- 65@LB@
46	0.003168	0.2306	b3066	dnaG	-7.10	0.407270	188 -- 205	41 -- 63	DNA primase	_____________187_____________________206\n_____________\|_______________________\|\n5'-ACC...UGCUA____________CU_________UGGAC...GCA-3'\n______________AAAAUCGG_GGC______AUGGC\n______________\|\|\|\|\|\|:\|_\|\|\|______\|\|\|\|\|\n______________UUUUAGUC_CCG______UACCG\n3'-UUU...CAACC________A___UUACGU_____GGUUG...UUG-5'\n_____________\|_______________________\|\n_____________64______________________40\n	189 -- 195	56 -- 62	-16.4791 kcal/mol	5.10709 kcal/mol	4.27657 kcal/mol	187 206@LB@ \| \|@LB@5'-ACC...UGCUA CU UGGAC...GCA-3'@LB@ AAAAUCGG GGC AUGGC@LB@ \|\|\|\|\|\|:\| \|\|\| \|\|\|\|\|@LB@ UUUUAGUC CCG UACCG@LB@3'-UUU...CAACC A UUACGU GGUUG...UUG-5'@LB@ \| \|@LB@ 64 40@LB@@LB@@LB@Energy -7.10 kcal/mol@LB@Hybridization Energy -16.4791 kcal/mol@LB@Unfolding Energy - mRNA 5.10709 kcal/mol@LB@Unfolding Energy - sRNA 4.27657 kcal/mol@LB@@LB@Position - mRNA 188 -- 205@LB@Position - sRNA 41 -- 63@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 56 -- 62@LB@
72	0.005975	0.2791	b1062	pyrC	-13.01	0.025478	15 -- 31	41 -- 58	dihydro-orotase	_____________14_________________32\n_____________\|__________________\|\n5'-GCG...GCAGC_________A________GAAAA...CCA-3'\n______________CAG_GGCGA_GCAAUGGC\n______________\|\|\|_\|\|\|:\|_\|\|\|\|\|\|\|\|\n______________GUC_CCGUU_CGUUACCG\n3'-UUU...UUUUA___A_____A________GGUUG...UUG-5'\n_____________\|__________________\|\n_____________59_________________40\n	25 -- 31	41 -- 47	-24.8377 kcal/mol	7.56192 kcal/mol	4.26806 kcal/mol	14 32@LB@ \| \|@LB@5'-GCG...GCAGC A GAAAA...CCA-3'@LB@ CAG GGCGA GCAAUGGC@LB@ \|\|\| \|\|\|:\| \|\|\|\|\|\|\|\|@LB@ GUC CCGUU CGUUACCG@LB@3'-UUU...UUUUA A A GGUUG...UUG-5'@LB@ \| \|@LB@ 59 40@LB@@LB@@LB@Energy -13.01 kcal/mol@LB@Hybridization Energy -24.8377 kcal/mol@LB@Unfolding Energy - mRNA 7.56192 kcal/mol@LB@Unfolding Energy - sRNA 4.26806 kcal/mol@LB@@LB@Position - mRNA 15 -- 31@LB@Position - sRNA 41 -- 58@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 41 -- 47@LB@
76	0.006626	0.2822	b1658	purR	-10.59	0.091499	175 -- 205	41 -- 63	transcriptional repressor hypoxanthine-binding	_____________174______________________________206\n_____________\|________________________________\|\n5'-UUU...GAGCU____________CUGGAGUGA____G______AACAA...GCA-3'\n______________GAAGUUAG_GGU_________AAUG_AAUGGC\n______________:\|\|:\|:\|\|_\|\|:_________\|\|\|\|_\|\|\|\|\|\|\n______________UUUUAGUC_CCG_________UUAC_UUACCG\n3'-UUU...CAACC________A________________G______GGUUG...UUG-5'\n_____________\|________________________________\|\n_____________64_______________________________40\n	176 -- 182	56 -- 62	-19.9152 kcal/mol	5.04846 kcal/mol	4.27657 kcal/mol	174 206@LB@ \| \|@LB@5'-UUU...GAGCU CUGGAGUGA G AACAA...GCA-3'@LB@ GAAGUUAG GGU AAUG AAUGGC@LB@ :\|\|:\|:\|\| \|\|: \|\|\|\| \|\|\|\|\|\|@LB@ UUUUAGUC CCG UUAC UUACCG@LB@3'-UUU...CAACC A G GGUUG...UUG-5'@LB@ \| \|@LB@ 64 40@LB@@LB@@LB@Energy -10.59 kcal/mol@LB@Hybridization Energy -19.9152 kcal/mol@LB@Unfolding Energy - mRNA 5.04846 kcal/mol@LB@Unfolding Energy - sRNA 4.27657 kcal/mol@LB@@LB@Position - mRNA 175 -- 205@LB@Position - sRNA 41 -- 63@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 56 -- 62@LB@
85	0.007532	0.2889	b4252	tabA	-7.64	0.334848	14 -- 22	41 -- 49	biofilm modulator regulated by toxins; DUF386 family protein cupin superfamily protein	_____________13________23\n_____________\|_________\|\n5'-UCU...ACAGC_________GGGGG...CAA-3'\n______________UGCAAUGGC\n______________\|\|\|\|\|\|\|\|\|\n______________ACGUUACCG\n3'-UUU...CCGUU_________GGUUG...UUG-5'\n_____________\|_________\|\n_____________50________40\n	16 -- 22	41 -- 47	-14.0816 kcal/mol	4.16801 kcal/mol	2.27678 kcal/mol	13 23@LB@ \| \|@LB@5'-UCU...ACAGC GGGGG...CAA-3'@LB@ UGCAAUGGC@LB@ \|\|\|\|\|\|\|\|\|@LB@ ACGUUACCG@LB@3'-UUU...CCGUU GGUUG...UUG-5'@LB@ \| \|@LB@ 50 40@LB@@LB@@LB@Energy -7.64 kcal/mol@LB@Hybridization Energy -14.0816 kcal/mol@LB@Unfolding Energy - mRNA 4.16801 kcal/mol@LB@Unfolding Energy - sRNA 2.27678 kcal/mol@LB@@LB@Position - mRNA 14 -- 22@LB@Position - sRNA 41 -- 49@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 41 -- 47@LB@
91	0.007817	0.2889	b3380	yhfW	-10.82	0.081759	179 -- 205	41 -- 67	phosphopentomutase-related metalloenzyme superfamily protein	_____________178_________________________206\n_____________\|___________________________\|\n5'-CUC...CAGUC_______C__UC___G__C________GCGAU...GUG-3'\n______________UUGGAAA_UC__UGG_GG_GUAAUGGC\n______________\|\|\|\|\|\|\|_\|\|__\|\|\|_::_\|:\|\|\|\|\|\|\n______________AACCUUU_AG__ACC_UU_CGUUACCG\n3'-UUU...UAUAC_______U__UC___G__A________GGUUG...UUG-5'\n_____________\|___________________________\|\n_____________68__________________________40\n	199 -- 205	41 -- 47	-26.7792 kcal/mol	10.1319 kcal/mol	5.83043 kcal/mol	178 206@LB@ \| \|@LB@5'-CUC...CAGUC C UC G C GCGAU...GUG-3'@LB@ UUGGAAA UC UGG GG GUAAUGGC@LB@ \|\|\|\|\|\|\| \|\| \|\|\| :: \|:\|\|\|\|\|\|@LB@ AACCUUU AG ACC UU CGUUACCG@LB@3'-UUU...UAUAC U UC G A GGUUG...UUG-5'@LB@ \| \|@LB@ 68 40@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -26.7792 kcal/mol@LB@Unfolding Energy - mRNA 10.1319 kcal/mol@LB@Unfolding Energy - sRNA 5.83043 kcal/mol@LB@@LB@Position - mRNA 179 -- 205@LB@Position - sRNA 41 -- 67@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 41 -- 47@LB@
94	0.008385	0.3	b1804	rnd	-8.17	0.271836	224 -- 238	41 -- 54	ribonuclease D	_____________223_____________239\n_____________\|_______________\|\n5'-GUC...ACCAC__A_______C____UUCUU...GUA-3'\n______________GG_CGAUGCG_UGGC\n______________\|\|_\|:\|\|\|\|:_\|\|\|\|\n______________CC_GUUACGU_ACCG\n3'-UUU...AGUCA__________U____GGUUG...UUG-5'\n_____________\|_______________\|\n_____________55______________40\n	227 -- 233	46 -- 52	-18.0571 kcal/mol	5.99437 kcal/mol	3.89026 kcal/mol	223 239@LB@ \| \|@LB@5'-GUC...ACCAC A C UUCUU...GUA-3'@LB@ GG CGAUGCG UGGC@LB@ \|\| \|:\|\|\|\|: \|\|\|\|@LB@ CC GUUACGU ACCG@LB@3'-UUU...AGUCA U GGUUG...UUG-5'@LB@ \| \|@LB@ 55 40@LB@@LB@@LB@Energy -8.17 kcal/mol@LB@Hybridization Energy -18.0571 kcal/mol@LB@Unfolding Energy - mRNA 5.99437 kcal/mol@LB@Unfolding Energy - sRNA 3.89026 kcal/mol@LB@@LB@Position - mRNA 224 -- 238@LB@Position - sRNA 41 -- 54@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 46 -- 52@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)

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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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