Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
5	9.512e-06	0.006694	b4006	purH	-17.40	0.004319	188 -- 204	31 -- 46	IMP cyclohydrolase and phosphoribosylaminoimidazolecarboxamide formyltransferase	_____________187_______________205\n_____________\|_________________\|\n5'-GUA...AAAUC__________A______AACAA...AGC-3'\n______________CAGGGGAUUU_CCAUGC\n______________\|\|\|\|\|\|\|\|\|\|_\|\|\|\|\|\|\n______________GUCCCCUAAA_GGUACG\n3'-UUU...AGUGA_________________AAUAU...GCA-5'\n_____________\|_________________\|\n_____________47________________30\n	191 -- 197	37 -- 43	-27.6893 kcal/mol	6.33421 kcal/mol	3.95768 kcal/mol	187 205@LB@ \| \|@LB@5'-GUA...AAAUC A AACAA...AGC-3'@LB@ CAGGGGAUUU CCAUGC@LB@ \|\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ GUCCCCUAAA GGUACG@LB@3'-UUU...AGUGA AAUAU...GCA-5'@LB@ \| \|@LB@ 47 30@LB@@LB@@LB@Energy -17.40 kcal/mol@LB@Hybridization Energy -27.6893 kcal/mol@LB@Unfolding Energy - mRNA 6.33421 kcal/mol@LB@Unfolding Energy - sRNA 3.95768 kcal/mol@LB@@LB@Position - mRNA 188 -- 204@LB@Position - sRNA 31 -- 46@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 37 -- 43@LB@
9	4.743e-05	0.01855	b1204	pth	-17.38	0.004387	162 -- 190	43 -- 74	peptidyl-tRNA hydrolase	_____________161_______________________________191\n_____________\|_________________________________\|\n5'-UGG...AGUAA________________A_____ACA________ACAAA...AGC-3'\n______________ACUACGCGC__CAGUU___UGU___CACUCAGG\n______________\|\|\|\|\|:\|:\|__\|\|:\|\|___\|\|\|___\|\|\|\|\|\|\|\|\n______________UGAUGUGUG__GUUAA___ACA___GUGAGUCC\n3'-UUU...GUUUC_________UC_____GCA___AA_________CCUAA...GCA-5'\n_____________\|_________________________________\|\n_____________75________________________________42\n	184 -- 190	43 -- 49	-27.969 kcal/mol	6.24318 kcal/mol	4.35222 kcal/mol	161 191@LB@ \| \|@LB@5'-UGG...AGUAA A ACA ACAAA...AGC-3'@LB@ ACUACGCGC CAGUU UGU CACUCAGG@LB@ \|\|\|\|\|:\|:\| \|\|:\|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ UGAUGUGUG GUUAA ACA GUGAGUCC@LB@3'-UUU...GUUUC UC GCA AA CCUAA...GCA-5'@LB@ \| \|@LB@ 75 42@LB@@LB@@LB@Energy -17.38 kcal/mol@LB@Hybridization Energy -27.969 kcal/mol@LB@Unfolding Energy - mRNA 6.24318 kcal/mol@LB@Unfolding Energy - sRNA 4.35222 kcal/mol@LB@@LB@Position - mRNA 162 -- 190@LB@Position - sRNA 43 -- 74@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 43 -- 49@LB@
28	0.0004009	0.04965	b3511	hdeD	-17.16	0.005105	126 -- 176	35 -- 75	acid-resistance membrane protein	_____________125__________________________________________________177\n_____________\|____________________________________________________\|\n5'-GAG...AAAUC________U_UUA__CG________G__AUAGAUUGAUAG____________UUCUU...UCG-3'\n______________GACUGCAU_C___GA__CGUU_UUU_GC____________CAGGGGAUUUUC\n______________\|\|\|\|:\|\|:_\|___:\|__\|\|\|\|_\|\|\|_:\|____________\|\|\|\|\|\|\|\|\|\|:\|\n______________CUGAUGUG_G___UU__GCAA_AAA_UG____________GUCCCCUAAAGG\n3'-UUU...CGUUU________U_UCG__AA____C___G__A_______________________UACGA...GCA-5'\n_____________\|____________________________________________________\|\n_____________76___________________________________________________34\n	170 -- 176	35 -- 41	-34.0299 kcal/mol	12.0619 kcal/mol	4.80541 kcal/mol	125 177@LB@ \| \|@LB@5'-GAG...AAAUC U UUA CG G AUAGAUUGAUAG UUCUU...UCG-3'@LB@ GACUGCAU C GA CGUU UUU GC CAGGGGAUUUUC@LB@ \|\|\|\|:\|\|: \| :\| \|\|\|\| \|\|\| :\| \|\|\|\|\|\|\|\|\|\|:\|@LB@ CUGAUGUG G UU GCAA AAA UG GUCCCCUAAAGG@LB@3'-UUU...CGUUU U UCG AA C G A UACGA...GCA-5'@LB@ \| \|@LB@ 76 34@LB@@LB@@LB@Energy -17.16 kcal/mol@LB@Hybridization Energy -34.0299 kcal/mol@LB@Unfolding Energy - mRNA 12.0619 kcal/mol@LB@Unfolding Energy - sRNA 4.80541 kcal/mol@LB@@LB@Position - mRNA 126 -- 176@LB@Position - sRNA 35 -- 75@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 35 -- 41@LB@
10	6.564e-05	0.0231	b3458	livK	-17.14	0.005196	153 -- 196	35 -- 71	leucine transporter subunit	_____________152____________________________________________197\n_____________\|______________________________________________\|\n5'-UGU...UGUUA______AAAAACAA_____CACAACA______GAAU__________GACUA...CGA-3'\n______________ACACAU________AGCAA_________UCAC____GGGGAUUUUU\n______________\|\|\|\|\|:________\|\|\|\|\|_________\|\|\|\|____\|\|\|\|\|\|\|\|::\n______________UGUGUG________UCGUU_________AGUG____CCCCUAAAGG\n3'-UUU...UCUGA___________________AAGCAACAA____AGU___________UACGA...GCA-5'\n_____________\|______________________________________________\|\n_____________72_____________________________________________34\n	190 -- 196	35 -- 41	-26.3585 kcal/mol	4.43917 kcal/mol	4.78171 kcal/mol	152 197@LB@ \| \|@LB@5'-UGU...UGUUA AAAAACAA CACAACA GAAU GACUA...CGA-3'@LB@ ACACAU AGCAA UCAC GGGGAUUUUU@LB@ \|\|\|\|\|: \|\|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\|::@LB@ UGUGUG UCGUU AGUG CCCCUAAAGG@LB@3'-UUU...UCUGA AAGCAACAA AGU UACGA...GCA-5'@LB@ \| \|@LB@ 72 34@LB@@LB@@LB@Energy -17.14 kcal/mol@LB@Hybridization Energy -26.3585 kcal/mol@LB@Unfolding Energy - mRNA 4.43917 kcal/mol@LB@Unfolding Energy - sRNA 4.78171 kcal/mol@LB@@LB@Position - mRNA 153 -- 196@LB@Position - sRNA 35 -- 71@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 35 -- 41@LB@
37	0.0006599	0.0618	b3399	yrfG	-16.99	0.005777	176 -- 197	35 -- 56	GMP/IMP nucleotidase	_____________175____________________198\n_____________\|______________________\|\n5'-UAG...GCAAA___C_______U__A_______CUCAU...AGC-3'\n______________UUG_UUCACUC_GG_GAUUUCC\n______________\|\|\|_\|\|\|\|\|\|\|_\|\|_\|\|\|\|\|\|\|\n______________AAC_AAGUGAG_CC_CUAAAGG\n3'-UUU...UAAGC___A_______U__C_______UACGA...GCA-5'\n_____________\|______________________\|\n_____________57_____________________34\n	191 -- 197	35 -- 41	-24.095 kcal/mol	5.08619 kcal/mol	2.02101 kcal/mol	175 198@LB@ \| \|@LB@5'-UAG...GCAAA C U A CUCAU...AGC-3'@LB@ UUG UUCACUC GG GAUUUCC@LB@ \|\|\| \|\|\|\|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ AAC AAGUGAG CC CUAAAGG@LB@3'-UUU...UAAGC A U C UACGA...GCA-5'@LB@ \| \|@LB@ 57 34@LB@@LB@@LB@Energy -16.99 kcal/mol@LB@Hybridization Energy -24.095 kcal/mol@LB@Unfolding Energy - mRNA 5.08619 kcal/mol@LB@Unfolding Energy - sRNA 2.02101 kcal/mol@LB@@LB@Position - mRNA 176 -- 197@LB@Position - sRNA 35 -- 56@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 35 -- 41@LB@
2	1.464e-07	0.0002576	b2741	rpoS	-16.90	0.006155	67 -- 107	33 -- 71	RNA polymerase sigma S (sigma 38) factor	_____________66______________________________________________108\n_____________\|_______________________________________________\|\n5'-CGG...GUUCA______UU___UUUUGAA______________A_______AA_____AAACC...AGG-3'\n______________ACACGC__GCA_______AUUCGUU_____AC__AGGGGA__UCCGU\n______________\|\|\|\|:\|__\|\|\|_______\|\|\|\|\|\|\|_____\|\|__\|\|\|\|\|\|__\|\|\|:\|\n______________UGUGUG__CGU_______UAAGCAA_____UG__UCCCCU__AGGUA\n3'-UUU...UCUGA______U__________________CAAAG__AG______AA_____CGAAU...GCA-5'\n_____________\|_______________________________________________\|\n_____________72______________________________________________32\n	85 -- 91	55 -- 61	-29.972 kcal/mol	8.28292 kcal/mol	4.7924 kcal/mol	66 108@LB@ \| \|@LB@5'-CGG...GUUCA UU UUUUGAA A AA AAACC...AGG-3'@LB@ ACACGC GCA AUUCGUU AC AGGGGA UCCGU@LB@ \|\|\|\|:\| \|\|\| \|\|\|\|\|\|\| \|\| \|\|\|\|\|\| \|\|\|:\|@LB@ UGUGUG CGU UAAGCAA UG UCCCCU AGGUA@LB@3'-UUU...UCUGA U CAAAG AG AA CGAAU...GCA-5'@LB@ \| \|@LB@ 72 32@LB@@LB@@LB@Energy -16.90 kcal/mol@LB@Hybridization Energy -29.972 kcal/mol@LB@Unfolding Energy - mRNA 8.28292 kcal/mol@LB@Unfolding Energy - sRNA 4.7924 kcal/mol@LB@@LB@Position - mRNA 67 -- 107@LB@Position - sRNA 33 -- 71@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 55 -- 61@LB@
45	0.001296	0.1014	b2465	tktB	-16.90	0.006168	210 -- 248	39 -- 78	transketolase 2 thiamine triphosphate-binding	_____________209__________________________________________249\n_____________\|____________________________________________\|\n5'-AGU...CCCGA______CU______AU________CG___________UAU____GCGGU...CUG-3'\n______________AAAGAC__UGC_CA__GCGAUUCG______CACUCAG___GGAU\n______________\|\|\|\|\|\|__\|:\|_\|\|__\|\|:\|\|\|\|\|______\|\|\|\|\|\|\|___\|\|\|\|\n______________UUUCUG__AUG_GU__CGUUAAGC______GUGAGUC___CCUA\n3'-UUU...ACCCG___________U__GU________AACAAA_______C______AAGGU...GCA-5'\n_____________\|____________________________________________\|\n_____________79___________________________________________38\n	235 -- 241	44 -- 50	-32.1578 kcal/mol	10.4844 kcal/mol	4.77966 kcal/mol	209 249@LB@ \| \|@LB@5'-AGU...CCCGA CU AU CG UAU GCGGU...CUG-3'@LB@ AAAGAC UGC CA GCGAUUCG CACUCAG GGAU@LB@ \|\|\|\|\|\| \|:\| \|\| \|\|:\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|@LB@ UUUCUG AUG GU CGUUAAGC GUGAGUC CCUA@LB@3'-UUU...ACCCG U GU AACAAA C AAGGU...GCA-5'@LB@ \| \|@LB@ 79 38@LB@@LB@@LB@Energy -16.90 kcal/mol@LB@Hybridization Energy -32.1578 kcal/mol@LB@Unfolding Energy - mRNA 10.4844 kcal/mol@LB@Unfolding Energy - sRNA 4.77966 kcal/mol@LB@@LB@Position - mRNA 210 -- 248@LB@Position - sRNA 39 -- 78@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 44 -- 50@LB@
57	0.002011	0.1223	b3057	bacA	-16.67	0.007222	149 -- 193	41 -- 71	undecaprenyl pyrophosphate phosphatase	_____________148___________________________________________194\n_____________\|_____________________________________________\|\n5'-UUC...UGGUC_______________GACAAG_GGUACAUUUUAAUA_________UUUAU...UUG-3'\n______________AUACGCAGUAGUUCG______C______________AUUUAGGGG\n______________\|:\|\|:\|\|\|:\|:\|\|\|\|______\|______________\|:\|:\|\|\|\|\|\n______________UGUGUGUCGUUAAGC______G______________UGAGUCCCC\n3'-UUU...UCUGA_______________AACAAA________________________UAAAG...GCA-5'\n_____________\|_____________________________________________\|\n_____________72____________________________________________40\n	187 -- 193	41 -- 47	-30.087 kcal/mol	8.67993 kcal/mol	4.74226 kcal/mol	148 194@LB@ \| \|@LB@5'-UUC...UGGUC GACAAG GGUACAUUUUAAUA UUUAU...UUG-3'@LB@ AUACGCAGUAGUUCG C AUUUAGGGG@LB@ \|:\|\|:\|\|\|:\|:\|\|\|\| \| \|:\|:\|\|\|\|\|@LB@ UGUGUGUCGUUAAGC G UGAGUCCCC@LB@3'-UUU...UCUGA AACAAA UAAAG...GCA-5'@LB@ \| \|@LB@ 72 40@LB@@LB@@LB@Energy -16.67 kcal/mol@LB@Hybridization Energy -30.087 kcal/mol@LB@Unfolding Energy - mRNA 8.67993 kcal/mol@LB@Unfolding Energy - sRNA 4.74226 kcal/mol@LB@@LB@Position - mRNA 149 -- 193@LB@Position - sRNA 41 -- 71@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 41 -- 47@LB@
15	0.0001044	0.0245	b0741	pal	-16.61	0.007509	30 -- 75	30 -- 71	peptidoglycan-associated outer membrane lipoprotein	_____________29_____________________________________________76\n_____________\|______________________________________________\|\n5'-GGA...UAACG____U________CUACAGCUCUU__________GGGA________GAAUU...GCG-3'\n______________GCAC_AUGGUAAU___________CUCAGGGGAU____UCCGUGCU\n______________:\|\|\|_\|::\|:\|\|\|___________\|\|\|\|\|\|\|\|\|\|____\|\|\|:\|\|\|\|\n______________UGUG_UGUCGUUA___________GAGUCCCCUA____AGGUACGA\n3'-UUU...UCUGA_____________AGCAACAAAGU__________A___________AUAUU...GCA-5'\n_____________\|______________________________________________\|\n_____________72_____________________________________________29\n	69 -- 75	30 -- 36	-38.4662 kcal/mol	13.7923 kcal/mol	8.066 kcal/mol	29 76@LB@ \| \|@LB@5'-GGA...UAACG U CUACAGCUCUU GGGA GAAUU...GCG-3'@LB@ GCAC AUGGUAAU CUCAGGGGAU UCCGUGCU@LB@ :\|\|\| \|::\|:\|\|\| \|\|\|\|\|\|\|\|\|\| \|\|\|:\|\|\|\|@LB@ UGUG UGUCGUUA GAGUCCCCUA AGGUACGA@LB@3'-UUU...UCUGA AGCAACAAAGU A AUAUU...GCA-5'@LB@ \| \|@LB@ 72 29@LB@@LB@@LB@Energy -16.61 kcal/mol@LB@Hybridization Energy -38.4662 kcal/mol@LB@Unfolding Energy - mRNA 13.7923 kcal/mol@LB@Unfolding Energy - sRNA 8.066 kcal/mol@LB@@LB@Position - mRNA 30 -- 75@LB@Position - sRNA 30 -- 71@LB@Position Seed - mRNA 69 -- 75@LB@Position Seed - sRNA 30 -- 36@LB@
115	0.005088	0.155	b4131	cadA	-16.57	0.007707	197 -- 237	37 -- 75	lysine decarboxylase acid-inducible	_____________196__________________________________________238\n_____________\|____________________________________________\|\n5'-CUC...GAUAU______GA___UUAUU_____A_____AA____AU_________AUUUU...UUG-3'\n______________GACUAU__ACG_____GCAAU___UUG__UCAC___GGGGGUUU\n______________\|\|\|\|\|:__\|\|:_____\|\|\|\|\|___\|\|\|__\|\|\|\|___\|\|\|\|:\|\|\|\n______________CUGAUG__UGU_____CGUUA___AAC__AGUG___CCCCUAAA\n3'-UUU...CGUUU______UG_____________AGC___AA____AGU________GGUAC...GCA-5'\n_____________\|____________________________________________\|\n_____________76___________________________________________36\n	231 -- 237	37 -- 43	-27.1465 kcal/mol	5.79755 kcal/mol	4.77966 kcal/mol	196 238@LB@ \| \|@LB@5'-CUC...GAUAU GA UUAUU A AA AU AUUUU...UUG-3'@LB@ GACUAU ACG GCAAU UUG UCAC GGGGGUUU@LB@ \|\|\|\|\|: \|\|: \|\|\|\|\| \|\|\| \|\|\|\| \|\|\|\|:\|\|\|@LB@ CUGAUG UGU CGUUA AAC AGUG CCCCUAAA@LB@3'-UUU...CGUUU UG AGC AA AGU GGUAC...GCA-5'@LB@ \| \|@LB@ 76 36@LB@@LB@@LB@Energy -16.57 kcal/mol@LB@Hybridization Energy -27.1465 kcal/mol@LB@Unfolding Energy - mRNA 5.79755 kcal/mol@LB@Unfolding Energy - sRNA 4.77966 kcal/mol@LB@@LB@Position - mRNA 197 -- 237@LB@Position - sRNA 37 -- 75@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 37 -- 43@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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