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
176	0.008803	0.1747	b1242	ychE	-11.39	0.137124	41 -- 64	45 -- 75	UPF0056 family inner membrane protein	_____________40______________________________65\n_____________\|_______________________________\|\n5'-CAU...UUGGU____________________________A__ACUAG...GCA-3'\n______________GGCUACAU_UAGCA______UGUUUUGC_CA\n______________\|:\|\|\|\|\|:_:\|\|\|\|______\|\|\|\|\|::\|_\|\|\n______________CUGAUGUG_GUCGU______ACAAAGUG_GU\n3'-UUU...CGUUU________U_____UAAGCA________A__CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	55 -- 61	48 -- 54	-19.9041 kcal/mol	4.77357 kcal/mol	3.74078 kcal/mol	40 65@LB@ \| \|@LB@5'-CAU...UUGGU A ACUAG...GCA-3'@LB@ GGCUACAU UAGCA UGUUUUGC CA@LB@ \|:\|\|\|\|\|: :\|\|\|\| \|\|\|\|\|::\| \|\|@LB@ CUGAUGUG GUCGU ACAAAGUG GU@LB@3'-UUU...CGUUU U UAAGCA A CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -11.39 kcal/mol@LB@Hybridization Energy -19.9041 kcal/mol@LB@Unfolding Energy - mRNA 4.77357 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 41 -- 64@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 55 -- 61@LB@Position Seed - sRNA 48 -- 54@LB@
133	0.006126	0.1605	b0387	yaiI	-9.01	0.350598	46 -- 81	33 -- 74	UPF0178 family protein	_____________45_________________________________________82\n_____________\|__________________________________________\|\n5'-CAC...CCCAU____________CAAUAAAACCG______UCU__________UGCCU...CAA-3'\n______________AUUGC_CGCAGC_____________AUUU______UUUCCAU\n______________\|:\|:\|_\|:\|\|\|\|_____________\|:\|:______\|\|\|\|\|\|\|\n______________UGAUG_GUGUCG_____________UGAG______AAAGGUA\n3'-UUU...GUUUC_____U______UUAAGCAACAAAG____UCCCCU_______CGAAU...GCA-5'\n_____________\|__________________________________________\|\n_____________75_________________________________________32\n	75 -- 81	33 -- 39	-16.9561 kcal/mol	3.12923 kcal/mol	4.81602 kcal/mol	45 82@LB@ \| \|@LB@5'-CAC...CCCAU CAAUAAAACCG UCU UGCCU...CAA-3'@LB@ AUUGC CGCAGC AUUU UUUCCAU@LB@ \|:\|:\| \|:\|\|\|\| \|:\|: \|\|\|\|\|\|\|@LB@ UGAUG GUGUCG UGAG AAAGGUA@LB@3'-UUU...GUUUC U UUAAGCAACAAAG UCCCCU CGAAU...GCA-5'@LB@ \| \|@LB@ 75 32@LB@@LB@@LB@Energy -9.01 kcal/mol@LB@Hybridization Energy -16.9561 kcal/mol@LB@Unfolding Energy - mRNA 3.12923 kcal/mol@LB@Unfolding Energy - sRNA 4.81602 kcal/mol@LB@@LB@Position - mRNA 46 -- 81@LB@Position - sRNA 33 -- 74@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 33 -- 39@LB@
27	0.0003358	0.04376	b1784	yeaH	-12.48	0.082239	130 -- 197	41 -- 99	UPF0229 family protein	_____________129___________________________________________________________________198\n_____________\|_____________________________________________________________________\|\n5'-UGU...ACGAC___GAAC______CCUG___A_C_____CAC____GUA_________UGGCAAA___AG___G______CAUAU...CGA-3'\n______________AGC____CGUGGG____AGA_G_GGCAA___AGGC___GCAUACAGU_______UGU__UAC__GGGGG\n______________\|\|\|____\|\|\|\|\|\|____\|\|\|_\|_\|\|\|\|\|___\|\|:\|___:\|\|:\|\|\|\|:_______\|\|\|__:\|\|__:\|\|\|\|\n______________UCG____GCACCC____UCU_C_CCGUU___UCUG___UGUGUGUCG_______ACA__GUG__UCCCC\n_____3'-UUUUUU___GGUA_____________A______________A___________UUAAGCA___AA___AG_____UAAAG...GCA-5'\n_____________\|_____________________________________________________________________\|\n_____________100___________________________________________________________________40\n	170 -- 176	63 -- 69	-48.2653 kcal/mol	18.2122 kcal/mol	17.5731 kcal/mol	129 198@LB@ \| \|@LB@5'-UGU...ACGAC GAAC CCUG A C CAC GUA UGGCAAA AG G CAUAU...CGA-3'@LB@ AGC CGUGGG AGA G GGCAA AGGC GCAUACAGU UGU UAC GGGGG@LB@ \|\|\| \|\|\|\|\|\| \|\|\| \| \|\|\|\|\| \|\|:\| :\|\|:\|\|\|\|: \|\|\| :\|\| :\|\|\|\|@LB@ UCG GCACCC UCU C CCGUU UCUG UGUGUGUCG ACA GUG UCCCC@LB@ 3'-UUUUUU GGUA A A UUAAGCA AA AG UAAAG...GCA-5'@LB@ \| \|@LB@ 100 40@LB@@LB@@LB@Energy -12.48 kcal/mol@LB@Hybridization Energy -48.2653 kcal/mol@LB@Unfolding Energy - mRNA 18.2122 kcal/mol@LB@Unfolding Energy - sRNA 17.5731 kcal/mol@LB@@LB@Position - mRNA 130 -- 197@LB@Position - sRNA 41 -- 99@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 63 -- 69@LB@
77	0.003184	0.1452	b4406	yaeP	-9.70	0.274250	222 -- 254	40 -- 71	UPF0253 family protein	_____________221________________________________255\n_____________\|__________________________________\|\n5'-ACC...AGUUA_______A_____A__CG_AAA________C___GACUU...UGC-3'\n______________AUACGCA_GCGGU_CG__G___UCGC_CAG_GGA\n______________\|:\|\|:\|\|_\|\|::\|_\|\|__\|___\|\|:\|_\|\|\|_\|\|\|\n______________UGUGUGU_CGUUA_GC__C___AGUG_GUC_CCU\n3'-UUU...UCUGA_____________A__AA_AA_____A___C___AAAGG...GCA-5'\n_____________\|__________________________________\|\n_____________72_________________________________39\n	222 -- 228	65 -- 71	-25.8836 kcal/mol	11.435 kcal/mol	4.74818 kcal/mol	221 255@LB@ \| \|@LB@5'-ACC...AGUUA A A CG AAA C GACUU...UGC-3'@LB@ AUACGCA GCGGU CG G UCGC CAG GGA@LB@ \|:\|\|:\|\| \|\|::\| \|\| \| \|\|:\| \|\|\| \|\|\|@LB@ UGUGUGU CGUUA GC C AGUG GUC CCU@LB@3'-UUU...UCUGA A AA AA A C AAAGG...GCA-5'@LB@ \| \|@LB@ 72 39@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -25.8836 kcal/mol@LB@Unfolding Energy - mRNA 11.435 kcal/mol@LB@Unfolding Energy - sRNA 4.74818 kcal/mol@LB@@LB@Position - mRNA 222 -- 254@LB@Position - sRNA 40 -- 71@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 65 -- 71@LB@
144	0.006569	0.1605	b2900	yqfB	-12.46	0.083290	200 -- 238	34 -- 70	UPF0267 family protein	_____________199_______________________________________239\n_____________\|_________________________________________\|\n5'-UUC...AGUAC________CAAA__ACA________UUUUUCAAC_______GGAUG...UCA-3'\n______________CAUGCAGC____CG_____UCACUU_________GUUUCCA\n______________\|\|::\|\|\|\|____\|\|_____\|\|\|\|\|:_________:\|\|\|\|\|\|\n______________GUGUGUCG____GC_____AGUGAG_________UAAAGGU\n3'-UUU...CUGAU________UUAA__AACAA______UCCCC___________ACGAA...GCA-5'\n_____________\|_________________________________________\|\n_____________71________________________________________33\n	232 -- 238	34 -- 40	-21.1736 kcal/mol	3.92715 kcal/mol	4.79237 kcal/mol	199 239@LB@ \| \|@LB@5'-UUC...AGUAC CAAA ACA UUUUUCAAC GGAUG...UCA-3'@LB@ CAUGCAGC CG UCACUU GUUUCCA@LB@ \|\|::\|\|\|\| \|\| \|\|\|\|\|: :\|\|\|\|\|\|@LB@ GUGUGUCG GC AGUGAG UAAAGGU@LB@3'-UUU...CUGAU UUAA AACAA UCCCC ACGAA...GCA-5'@LB@ \| \|@LB@ 71 33@LB@@LB@@LB@Energy -12.46 kcal/mol@LB@Hybridization Energy -21.1736 kcal/mol@LB@Unfolding Energy - mRNA 3.92715 kcal/mol@LB@Unfolding Energy - sRNA 4.79237 kcal/mol@LB@@LB@Position - mRNA 200 -- 238@LB@Position - sRNA 34 -- 70@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 34 -- 40@LB@
129	0.005822	0.1577	b0713	ybgL	-14.99	0.021088	226 -- 247	61 -- 83	UPF0271 family protein	_____________225_____________________248\n_____________\|_______________________\|\n5'-GCC...CGAUC_______________________CGCAG...AUG-3'\n______________UGGGCGAAGGCUGCGC_CAGCGA\n______________\|\|\|\|\|:\|\|\|:\|\|:\|:\|_\|\|\|\|:\|\n______________ACCCGUUUCUGAUGUG_GUCGUU\n3'-UUU...CCUCU________________U______AAGCA...GCA-5'\n_____________\|_______________________\|\n_____________84______________________60\n	234 -- 240	69 -- 75	-36.9571 kcal/mol	11.7384 kcal/mol	10.2322 kcal/mol	225 248@LB@ \| \|@LB@5'-GCC...CGAUC CGCAG...AUG-3'@LB@ UGGGCGAAGGCUGCGC CAGCGA@LB@ \|\|\|\|\|:\|\|\|:\|\|:\|:\| \|\|\|\|:\|@LB@ ACCCGUUUCUGAUGUG GUCGUU@LB@3'-UUU...CCUCU U AAGCA...GCA-5'@LB@ \| \|@LB@ 84 60@LB@@LB@@LB@Energy -14.99 kcal/mol@LB@Hybridization Energy -36.9571 kcal/mol@LB@Unfolding Energy - mRNA 11.7384 kcal/mol@LB@Unfolding Energy - sRNA 10.2322 kcal/mol@LB@@LB@Position - mRNA 226 -- 247@LB@Position - sRNA 61 -- 83@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 69 -- 75@LB@
157	0.007641	0.1668	b3154	yhbP	-10.32	0.216043	188 -- 213	45 -- 78	UPF0306 family protein	_____________187________________________________214\n_____________\|__________________________________\|\n5'-AAA...GUAUA_____GA____________GGAAA__________UCGCC...UUU-3'\n______________AAAGA______ACAGCAAU_________CACUCA\n______________\|\|\|\|\|______\|\|\|\|\|\|\|\|_________\|\|\|\|\|\|\n______________UUUCU______UGUCGUUA_________GUGAGU\n3'-UUU...ACCCG_____GAUGUG________AGCAACAAA______CCCCU...GCA-5'\n_____________\|__________________________________\|\n_____________79_________________________________44\n	196 -- 202	60 -- 66	-17.2265 kcal/mol	3.1682 kcal/mol	3.741 kcal/mol	187 214@LB@ \| \|@LB@5'-AAA...GUAUA GA GGAAA UCGCC...UUU-3'@LB@ AAAGA ACAGCAAU CACUCA@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ UUUCU UGUCGUUA GUGAGU@LB@3'-UUU...ACCCG GAUGUG AGCAACAAA CCCCU...GCA-5'@LB@ \| \|@LB@ 79 44@LB@@LB@@LB@Energy -10.32 kcal/mol@LB@Hybridization Energy -17.2265 kcal/mol@LB@Unfolding Energy - mRNA 3.1682 kcal/mol@LB@Unfolding Energy - sRNA 3.741 kcal/mol@LB@@LB@Position - mRNA 188 -- 213@LB@Position - sRNA 45 -- 78@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 60 -- 66@LB@
166	0.008074	0.1711	b2158	yeiH	-9.26	0.321503	233 -- 257	41 -- 72	UPF0324 family inner membrane protein	_____________232_______________________________258\n_____________\|_________________________________\|\n5'-CAC...CAUCG_____UG_____________________C____UUAGC...GUG-3'\n______________UACAC__UGGCA________UUUUAUUC_GGGG\n______________\|\|\|\|\|__::\|\|\|________\|\|\|:\|:\|\|_\|\|\|\|\n______________AUGUG__GUCGU________AAAGUGAG_CCCC\n3'-UUU...UUCUG_____U______UAAGCAAC________U____UAAAG...GCA-5'\n_____________\|_________________________________\|\n_____________73________________________________40\n	246 -- 252	46 -- 52	-21.8619 kcal/mol	7.84401 kcal/mol	4.75632 kcal/mol	232 258@LB@ \| \|@LB@5'-CAC...CAUCG UG C UUAGC...GUG-3'@LB@ UACAC UGGCA UUUUAUUC GGGG@LB@ \|\|\|\|\| ::\|\|\| \|\|\|:\|:\|\| \|\|\|\|@LB@ AUGUG GUCGU AAAGUGAG CCCC@LB@3'-UUU...UUCUG U UAAGCAAC U UAAAG...GCA-5'@LB@ \| \|@LB@ 73 40@LB@@LB@@LB@Energy -9.26 kcal/mol@LB@Hybridization Energy -21.8619 kcal/mol@LB@Unfolding Energy - mRNA 7.84401 kcal/mol@LB@Unfolding Energy - sRNA 4.75632 kcal/mol@LB@@LB@Position - mRNA 233 -- 257@LB@Position - sRNA 41 -- 72@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 46 -- 52@LB@
109	0.004772	0.1538	b2580	ung	-9.28	0.319241	25 -- 55	36 -- 70	uracil-DNA-glycosylase	_____________24__________________________________56\n_____________\|___________________________________\|\n5'-UCU...AAAAC______U___GUA____G_____AAAU________AUUGU...CCG-3'\n______________CACACA_CAA_____UG__UCGC_____GGAUUUU\n______________\|\|\|\|\|\|_\|\|\|_____\|\|__\|\|:\|_____\|\|\|\|\|\|:\n______________GUGUGU_GUU_____AC__AGUG_____CCUAAAG\n3'-UUU...CUGAU______C___AAGCA__AA____AGUCC_______GUACG...GCA-5'\n_____________\|___________________________________\|\n_____________71__________________________________35\n	49 -- 55	36 -- 42	-19.0861 kcal/mol	5.04532 kcal/mol	4.7591 kcal/mol	24 56@LB@ \| \|@LB@5'-UCU...AAAAC U GUA G AAAU AUUGU...CCG-3'@LB@ CACACA CAA UG UCGC GGAUUUU@LB@ \|\|\|\|\|\| \|\|\| \|\| \|\|:\| \|\|\|\|\|\|:@LB@ GUGUGU GUU AC AGUG CCUAAAG@LB@3'-UUU...CUGAU C AAGCA AA AGUCC GUACG...GCA-5'@LB@ \| \|@LB@ 71 35@LB@@LB@@LB@Energy -9.28 kcal/mol@LB@Hybridization Energy -19.0861 kcal/mol@LB@Unfolding Energy - mRNA 5.04532 kcal/mol@LB@Unfolding Energy - sRNA 4.7591 kcal/mol@LB@@LB@Position - mRNA 25 -- 55@LB@Position - sRNA 36 -- 70@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 36 -- 42@LB@
151	0.007209	0.1668	b0968	yccX	-9.35	0.311742	266 -- 274	62 -- 70	weak acylphosphatase	_____________265_______275\n_____________\|_________\|\n5'-GGC...UACAC_________CGAAG...CCG-3'\n______________CACACAGUA\n______________\|\|\|\|\|\|\|:\|\n______________GUGUGUCGU\n3'-UUU...CUGAU_________UAAGC...GCA-5'\n_____________\|_________\|\n_____________71________61\n	268 -- 274	62 -- 68	-13.335 kcal/mol	0.836274 kcal/mol	3.14945 kcal/mol	265 275@LB@ \| \|@LB@5'-GGC...UACAC CGAAG...CCG-3'@LB@ CACACAGUA@LB@ \|\|\|\|\|\|\|:\|@LB@ GUGUGUCGU@LB@3'-UUU...CUGAU UAAGC...GCA-5'@LB@ \| \|@LB@ 71 61@LB@@LB@@LB@Energy -9.35 kcal/mol@LB@Hybridization Energy -13.335 kcal/mol@LB@Unfolding Energy - mRNA 0.836274 kcal/mol@LB@Unfolding Energy - sRNA 3.14945 kcal/mol@LB@@LB@Position - mRNA 266 -- 274@LB@Position - sRNA 62 -- 70@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 62 -- 68@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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