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
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@
93	0.004161	0.1538	b4221	tamB	-11.98	0.104509	154 -- 185	44 -- 78	translocation and assembly module for autotransporter export inner membrane subunit	_____________153__________________________________186\n_____________\|____________________________________\|\n5'-ACC...CGGAU______GA____________ACA________A____UCUGG...AUC-3'\n______________AAAGAC___ACACGG__GUU____GUUUUAC_UCGG\n______________\|\|\|\|\|\|___\|\|\|\|:\|__:\|\|____\|\|\|\|:\|\|_\|\|:\|\n______________UUUCUG___UGUGUC__UAA____CAAAGUG_AGUC\n3'-UUU...ACCCG______AUG______GU___GCAA____________CCCUA...GCA-5'\n_____________\|____________________________________\|\n_____________79___________________________________43\n	174 -- 180	48 -- 54	-22.2219 kcal/mol	6.10136 kcal/mol	4.13875 kcal/mol	153 186@LB@ \| \|@LB@5'-ACC...CGGAU GA ACA A UCUGG...AUC-3'@LB@ AAAGAC ACACGG GUU GUUUUAC UCGG@LB@ \|\|\|\|\|\| \|\|\|\|:\| :\|\| \|\|\|\|:\|\| \|\|:\|@LB@ UUUCUG UGUGUC UAA CAAAGUG AGUC@LB@3'-UUU...ACCCG AUG GU GCAA CCCUA...GCA-5'@LB@ \| \|@LB@ 79 43@LB@@LB@@LB@Energy -11.98 kcal/mol@LB@Hybridization Energy -22.2219 kcal/mol@LB@Unfolding Energy - mRNA 6.10136 kcal/mol@LB@Unfolding Energy - sRNA 4.13875 kcal/mol@LB@@LB@Position - mRNA 154 -- 185@LB@Position - sRNA 44 -- 78@LB@Position Seed - mRNA 174 -- 180@LB@Position Seed - sRNA 48 -- 54@LB@
183	0.009087	0.1747	b3965	trmA	-11.75	0.116675	18 -- 52	35 -- 74	tRNA m(5)U54 methyltransferase SAM-dependent; tmRNA m(5)U341 methyltransferase	_____________17____________________________________________53\n_____________\|_____________________________________________\|\n5'-UCG...UUACC________U____UCCA_________________________C__UAUUA...UUC-3'\n______________GCUGCGCG_CAGC____GAUUCG______CACU____GGAUU_CC\n______________:\|\|:\|:\|:_\|\|\|\|____:\|\|\|\|\|______\|\|\|\|____\|\|\|\|\|_\|\|\n______________UGAUGUGU_GUCG____UUAAGC______GUGA____CCUAA_GG\n3'-UUU...GUUUC_______________________AACAAA____GUCC_____A__UACGA...GCA-5'\n_____________\|_____________________________________________\|\n_____________75____________________________________________34\n	18 -- 24	68 -- 74	-28.5766 kcal/mol	12.0258 kcal/mol	4.80541 kcal/mol	17 53@LB@ \| \|@LB@5'-UCG...UUACC U UCCA C UAUUA...UUC-3'@LB@ GCUGCGCG CAGC GAUUCG CACU GGAUU CC@LB@ :\|\|:\|:\|: \|\|\|\| :\|\|\|\|\| \|\|\|\| \|\|\|\|\| \|\|@LB@ UGAUGUGU GUCG UUAAGC GUGA CCUAA GG@LB@3'-UUU...GUUUC AACAAA GUCC A UACGA...GCA-5'@LB@ \| \|@LB@ 75 34@LB@@LB@@LB@Energy -11.75 kcal/mol@LB@Hybridization Energy -28.5766 kcal/mol@LB@Unfolding Energy - mRNA 12.0258 kcal/mol@LB@Unfolding Energy - sRNA 4.80541 kcal/mol@LB@@LB@Position - mRNA 18 -- 52@LB@Position - sRNA 35 -- 74@LB@Position Seed - mRNA 18 -- 24@LB@Position Seed - sRNA 68 -- 74@LB@
44	0.001243	0.09943	b3064	tsaD	-15.06	0.020167	98 -- 131	41 -- 82	tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein; glycation binding protein	_____________97___________________________________________132\n_____________\|____________________________________________\|\n5'-CAU...UAUAA_________G_______GA________________U________CGAAC...UGA-3'\n______________GGGUGAGGA_UAUACAC__GGC_________UUUC_C_CAGGGG\n______________\|\|\|::\|:\|\|_\|\|:\|\|\|\|__:\|\|_________\|\|\|\|_\|_\|\|\|\|\|\|\n______________CCCGUUUCU_AUGUGUG__UCG_________AAAG_G_GUCCCC\n3'-UUU...CUCUA_________G____________UUAAGCAAC____U_A______UAAAG...GCA-5'\n_____________\|____________________________________________\|\n_____________83___________________________________________40\n	108 -- 114	66 -- 72	-38.4936 kcal/mol	9.4641 kcal/mol	13.9685 kcal/mol	97 132@LB@ \| \|@LB@5'-CAU...UAUAA G GA U CGAAC...UGA-3'@LB@ GGGUGAGGA UAUACAC GGC UUUC C CAGGGG@LB@ \|\|\|::\|:\|\| \|\|:\|\|\|\| :\|\| \|\|\|\| \| \|\|\|\|\|\|@LB@ CCCGUUUCU AUGUGUG UCG AAAG G GUCCCC@LB@3'-UUU...CUCUA G UUAAGCAAC U A UAAAG...GCA-5'@LB@ \| \|@LB@ 83 40@LB@@LB@@LB@Energy -15.06 kcal/mol@LB@Hybridization Energy -38.4936 kcal/mol@LB@Unfolding Energy - mRNA 9.4641 kcal/mol@LB@Unfolding Energy - sRNA 13.9685 kcal/mol@LB@@LB@Position - mRNA 98 -- 131@LB@Position - sRNA 41 -- 82@LB@Position Seed - mRNA 108 -- 114@LB@Position Seed - sRNA 66 -- 72@LB@
96	0.004462	0.1538	b3260	dusB	-10.19	0.227205	72 -- 117	38 -- 74	tRNA-dihydrouridine synthase B	_____________71_____________________________________________118\n_____________\|______________________________________________\|\n5'-ACU...AUCGC__C____U__UUUUAAAU_______U___AUC__U_____A_____GGUCA...GAG-3'\n______________AC_ACGC_CA________GCAAUUC_UUG___CA_CUCAG_GGAUU\n______________\|\|_\|\|:\|_\|\|________\|\|\|\|\|\|\|_\|\|\|___\|\|_\|\|\|\|\|_\|\|\|\|\|\n______________UG_UGUG_GU________CGUUAAG_AAC___GU_GAGUC_CCUAA\n3'-UUU...GUUUC__A____U_________________C___AAA________C_____AGGUA...GCA-5'\n_____________\|______________________________________________\|\n_____________75_____________________________________________37\n	90 -- 96	58 -- 64	-26.7161 kcal/mol	11.7467 kcal/mol	4.77867 kcal/mol	71 118@LB@ \| \|@LB@5'-ACU...AUCGC C U UUUUAAAU U AUC U A GGUCA...GAG-3'@LB@ AC ACGC CA GCAAUUC UUG CA CUCAG GGAUU@LB@ \|\| \|\|:\| \|\| \|\|\|\|\|\|\| \|\|\| \|\| \|\|\|\|\| \|\|\|\|\|@LB@ UG UGUG GU CGUUAAG AAC GU GAGUC CCUAA@LB@3'-UUU...GUUUC A U C AAA C AGGUA...GCA-5'@LB@ \| \|@LB@ 75 37@LB@@LB@@LB@Energy -10.19 kcal/mol@LB@Hybridization Energy -26.7161 kcal/mol@LB@Unfolding Energy - mRNA 11.7467 kcal/mol@LB@Unfolding Energy - sRNA 4.77867 kcal/mol@LB@@LB@Position - mRNA 72 -- 117@LB@Position - sRNA 38 -- 74@LB@Position Seed - mRNA 90 -- 96@LB@Position Seed - sRNA 58 -- 64@LB@
125	0.005556	0.1564	b3384	trpS	-12.26	0.091693	207 -- 244	40 -- 100	tryptophanyl-tRNA synthetase	_____________206___________________________________________________________245\n_____________\|_____________________________________________________________\|\n5'-ACA...UGACU___________UUUUA__________________________________________U__AUUGA...AUG-3'\n______________AAGCCCAUCGU_____GUGG__________CGCACAGC____________C_CUCAGG_GA\n______________\|\|\|\|\|\|\|\|\|\|\|_____:\|\|\|__________\|:\|\|\|\|\|\|____________\|_\|\|\|\|\|\|_\|\|\n______________UUCGGGUAGCA_____UACC__________GUGUGUCG____________G_GAGUCC_CU\n______3'-UUUUU___________CCCUC____CGUUUCUGAU________UUAAGCAACAAA_U______C__AAAGG...GCA-5'\n_____________\|_____________________________________________________________\|\n_____________101___________________________________________________________39\n	228 -- 234	63 -- 69	-41.2838 kcal/mol	11.4457 kcal/mol	17.5818 kcal/mol	206 245@LB@ \| \|@LB@5'-ACA...UGACU UUUUA U AUUGA...AUG-3'@LB@ AAGCCCAUCGU GUGG CGCACAGC C CUCAGG GA@LB@ \|\|\|\|\|\|\|\|\|\|\| :\|\|\| \|:\|\|\|\|\|\| \| \|\|\|\|\|\| \|\|@LB@ UUCGGGUAGCA UACC GUGUGUCG G GAGUCC CU@LB@ 3'-UUUUU CCCUC CGUUUCUGAU UUAAGCAACAAA U C AAAGG...GCA-5'@LB@ \| \|@LB@ 101 39@LB@@LB@@LB@Energy -12.26 kcal/mol@LB@Hybridization Energy -41.2838 kcal/mol@LB@Unfolding Energy - mRNA 11.4457 kcal/mol@LB@Unfolding Energy - sRNA 17.5818 kcal/mol@LB@@LB@Position - mRNA 207 -- 244@LB@Position - sRNA 40 -- 100@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 63 -- 69@LB@
31	0.0004964	0.05552	b2325	yfcL	-14.31	0.031288	272 -- 297	32 -- 57	uncharacterized protein	_____________271__________________________298\n_____________\|____________________________\|\n5'-AAC...GAUGA______________U___U____G____GCC-3'\n______________GUUGUUU_GC_CAG_GGG_AUUU_CGUG\n______________\|\|\|\|\|\|\|_:\|_\|\|\|_\|\|\|_\|\|\|\|_\|:\|\|\n______________CAACAAA_UG_GUC_CCC_UAAA_GUAC\n3'-UUU...UUAAG_______G__A____________G____GAAUA...GCA-5'\n_____________\|____________________________\|\n_____________58___________________________31\n	272 -- 278	51 -- 57	-23.7407 kcal/mol	4.96676 kcal/mol	4.4642 kcal/mol	271 298@LB@ \| \|@LB@5'-AAC...GAUGA U U G GCC-3'@LB@ GUUGUUU GC CAG GGG AUUU CGUG@LB@ \|\|\|\|\|\|\| :\| \|\|\| \|\|\| \|\|\|\| \|:\|\|@LB@ CAACAAA UG GUC CCC UAAA GUAC@LB@3'-UUU...UUAAG G A G GAAUA...GCA-5'@LB@ \| \|@LB@ 58 31@LB@@LB@@LB@Energy -14.31 kcal/mol@LB@Hybridization Energy -23.7407 kcal/mol@LB@Unfolding Energy - mRNA 4.96676 kcal/mol@LB@Unfolding Energy - sRNA 4.4642 kcal/mol@LB@@LB@Position - mRNA 272 -- 297@LB@Position - sRNA 32 -- 57@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 51 -- 57@LB@
48	0.001595	0.1153	b4567	yjjZ	-9.54	0.291590	92 -- 131	37 -- 74	uncharacterized protein	_____________91_______________________________________132\n_____________\|________________________________________\|\n5'-CGG...UGAUU____AU_________AG___UACC__AUAG__A_______AUCUG...GGA-3'\n______________GCUA__CAUAGCGAU__GUU____CG____CA_GGGAUUU\n______________:\|\|\|__\|\|:\|\|\|:\|\|__\|\|\|____\|:____\|\|_\|\|\|\|\|\|\|\n______________UGAU__GUGUCGUUA__CAA____GU____GU_CCCUAAA\n3'-UUU...GUUUC____GU_________AG___CAAA__GA____C_______GGUAC...GCA-5'\n_____________\|________________________________________\|\n_____________75_______________________________________36\n	125 -- 131	37 -- 43	-26.8907 kcal/mol	12.5776 kcal/mol	4.77887 kcal/mol	91 132@LB@ \| \|@LB@5'-CGG...UGAUU AU AG UACC AUAG A AUCUG...GGA-3'@LB@ GCUA CAUAGCGAU GUU CG CA GGGAUUU@LB@ :\|\|\| \|\|:\|\|\|:\|\| \|\|\| \|: \|\| \|\|\|\|\|\|\|@LB@ UGAU GUGUCGUUA CAA GU GU CCCUAAA@LB@3'-UUU...GUUUC GU AG CAAA GA C GGUAC...GCA-5'@LB@ \| \|@LB@ 75 36@LB@@LB@@LB@Energy -9.54 kcal/mol@LB@Hybridization Energy -26.8907 kcal/mol@LB@Unfolding Energy - mRNA 12.5776 kcal/mol@LB@Unfolding Energy - sRNA 4.77887 kcal/mol@LB@@LB@Position - mRNA 92 -- 131@LB@Position - sRNA 37 -- 74@LB@Position Seed - mRNA 125 -- 131@LB@Position Seed - sRNA 37 -- 43@LB@
156	0.007591	0.1668	b1044	ymdA	-16.39	0.008687	226 -- 252	46 -- 73	uncharacterized protein	_____________225__________________________253\n_____________\|____________________________\|\n5'-UGA...CUCUC______U____________U________UUAUU...UUU-3'\n______________UUAUGC_CGGCAGUUUGUU_UUUC_CUU\n______________:\|\|::\|_\|:\|\|\|:\|\|:\|\|\|_\|\|\|\|_\|\|:\n______________GAUGUG_GUCGUUAAGCAA_AAAG_GAG\n3'-UUU...UUUCU______U____________C____U___UCCCC...GCA-5'\n_____________\|____________________________\|\n_____________74___________________________45\n	236 -- 242	57 -- 63	-24.6333 kcal/mol	4.51706 kcal/mol	3.72492 kcal/mol	225 253@LB@ \| \|@LB@5'-UGA...CUCUC U U UUAUU...UUU-3'@LB@ UUAUGC CGGCAGUUUGUU UUUC CUU@LB@ :\|\|::\| \|:\|\|\|:\|\|:\|\|\| \|\|\|\| \|\|:@LB@ GAUGUG GUCGUUAAGCAA AAAG GAG@LB@3'-UUU...UUUCU U C U UCCCC...GCA-5'@LB@ \| \|@LB@ 74 45@LB@@LB@@LB@Energy -16.39 kcal/mol@LB@Hybridization Energy -24.6333 kcal/mol@LB@Unfolding Energy - mRNA 4.51706 kcal/mol@LB@Unfolding Energy - sRNA 3.72492 kcal/mol@LB@@LB@Position - mRNA 226 -- 252@LB@Position - sRNA 46 -- 73@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 57 -- 63@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@

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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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

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