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
14	0.0001025	0.0245	b4051	qorA	-14.73	0.024599	192 -- 224	48 -- 76	quinone oxidoreductase NADPH-dependent	_____________191_______________________________225\n_____________\|_________________________________\|\n5'-CGC...GUUCU___GG___________CA__AA___AA______AAGCA...UCG-3'\n______________GGA__ACACAUGGCAA__CG__UUG__UUUCAC\n______________:\|\|__\|\|\|\|\|::\|\|\|\|__\|\|__\|\|\|__\|\|\|\|\|\|\n______________UCU__UGUGUGUCGUU__GC__AAC__AAAGUG\n3'-UUU...CCGUU___GA___________AA_______________AGUCC...GCA-5'\n_____________\|_________________________________\|\n_____________77________________________________47\n	201 -- 207	61 -- 67	-23.6874 kcal/mol	5.27405 kcal/mol	3.68714 kcal/mol	191 225@LB@ \| \|@LB@5'-CGC...GUUCU GG CA AA AA AAGCA...UCG-3'@LB@ GGA ACACAUGGCAA CG UUG UUUCAC@LB@ :\|\| \|\|\|\|\|::\|\|\|\| \|\| \|\|\| \|\|\|\|\|\|@LB@ UCU UGUGUGUCGUU GC AAC AAAGUG@LB@3'-UUU...CCGUU GA AA AGUCC...GCA-5'@LB@ \| \|@LB@ 77 47@LB@@LB@@LB@Energy -14.73 kcal/mol@LB@Hybridization Energy -23.6874 kcal/mol@LB@Unfolding Energy - mRNA 5.27405 kcal/mol@LB@Unfolding Energy - sRNA 3.68714 kcal/mol@LB@@LB@Position - mRNA 192 -- 224@LB@Position - sRNA 48 -- 76@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 61 -- 67@LB@
18	0.0001516	0.02826	b2817	amiC	-14.62	0.026197	167 -- 204	31 -- 70	N-acetylmuramoyl-L-alanine amidase	_____________166______________________________________205\n_____________\|________________________________________\|\n5'-AGU...CUUGU________UUAGAUUUC___________A__GG_______CAGGA...UCA-3'\n______________UACACAGC_________UUUUGCUCGGG_GA____CAUGU\n______________:\|\|\|\|\|\|\|_________\|\|\|::\|\|\|:\|\|_\|\|____\|\|\|\|:\n______________GUGUGUCG_________AAAGUGAGUCC_CU____GUACG\n3'-UUU...CUGAU________UUAAGCAAC___________C__AAAG_____AAUAU...GCA-5'\n_____________\|________________________________________\|\n_____________71_______________________________________30\n	188 -- 194	43 -- 49	-32.0387 kcal/mol	10.1821 kcal/mol	7.23824 kcal/mol	166 205@LB@ \| \|@LB@5'-AGU...CUUGU UUAGAUUUC A GG CAGGA...UCA-3'@LB@ UACACAGC UUUUGCUCGGG GA CAUGU@LB@ :\|\|\|\|\|\|\| \|\|\|::\|\|\|:\|\| \|\| \|\|\|\|:@LB@ GUGUGUCG AAAGUGAGUCC CU GUACG@LB@3'-UUU...CUGAU UUAAGCAAC C AAAG AAUAU...GCA-5'@LB@ \| \|@LB@ 71 30@LB@@LB@@LB@Energy -14.62 kcal/mol@LB@Hybridization Energy -32.0387 kcal/mol@LB@Unfolding Energy - mRNA 10.1821 kcal/mol@LB@Unfolding Energy - sRNA 7.23824 kcal/mol@LB@@LB@Position - mRNA 167 -- 204@LB@Position - sRNA 31 -- 70@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 43 -- 49@LB@
49	0.00161	0.1153	b0655	gltI	-14.54	0.027470	112 -- 169	31 -- 74	glutamate/aspartate periplasmic binding protein	_____________111________________________________________________________170\n_____________\|__________________________________________________________\|\n5'-AUU...ACAAC_______AAUAAAGUU____A____AACAACACAAA______CAAC____A_______GUUCU...UGG-3'\n______________ACUGCAC_________GCAG_CGAU___________CACUCA____GGGU_UCCAUGC\n______________\|\|\|:\|\|\|_________:\|\|\|_\|:\|\|___________\|\|\|\|\|\|____\|\|:\|_\|\|\|\|\|\|\|\n______________UGAUGUG_________UGUC_GUUA___________GUGAGU____CCUA_AGGUACG\n3'-UUU...GUUUC_________________________AGCAACAAA________CC______A_______AAUAU...GCA-5'\n_____________\|__________________________________________________________\|\n_____________75_________________________________________________________30\n	163 -- 169	31 -- 37	-33.5884 kcal/mol	11.7902 kcal/mol	7.26183 kcal/mol	111 170@LB@ \| \|@LB@5'-AUU...ACAAC AAUAAAGUU A AACAACACAAA CAAC A GUUCU...UGG-3'@LB@ ACUGCAC GCAG CGAU CACUCA GGGU UCCAUGC@LB@ \|\|\|:\|\|\| :\|\|\| \|:\|\| \|\|\|\|\|\| \|\|:\| \|\|\|\|\|\|\|@LB@ UGAUGUG UGUC GUUA GUGAGU CCUA AGGUACG@LB@3'-UUU...GUUUC AGCAACAAA CC A AAUAU...GCA-5'@LB@ \| \|@LB@ 75 30@LB@@LB@@LB@Energy -14.54 kcal/mol@LB@Hybridization Energy -33.5884 kcal/mol@LB@Unfolding Energy - mRNA 11.7902 kcal/mol@LB@Unfolding Energy - sRNA 7.26183 kcal/mol@LB@@LB@Position - mRNA 112 -- 169@LB@Position - sRNA 31 -- 74@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 31 -- 37@LB@
192	0.00979	0.1776	b3879	yihR	-14.50	0.028125	239 -- 282	38 -- 72	putative sulphoquinovose mutarotase	_____________238__________________________________________283\n_____________\|____________________________________________\|\n5'-CAU...ACCAA_______U_____GGACAGACC________UGCCG_________AUCAC...UGA-3'\n______________UAUGCAU_GCAGU_________GUUUCACU_____CGGGGGAUU\n______________\|\|::\|\|:_\|\|\|:\|_________\|\|\|\|\|\|\|\|_____\|:\|\|\|\|\|\|\|\n______________AUGUGUG_CGUUA_________CAAAGUGA_____GUCCCCUAA\n3'-UUU...UUCUG_______U_____AGCAA__________________________AGGUA...GCA-5'\n_____________\|____________________________________________\|\n_____________73___________________________________________37\n	276 -- 282	38 -- 44	-32.397 kcal/mol	13.138 kcal/mol	4.76382 kcal/mol	238 283@LB@ \| \|@LB@5'-CAU...ACCAA U GGACAGACC UGCCG AUCAC...UGA-3'@LB@ UAUGCAU GCAGU GUUUCACU CGGGGGAUU@LB@ \|\|::\|\|: \|\|\|:\| \|\|\|\|\|\|\|\| \|:\|\|\|\|\|\|\|@LB@ AUGUGUG CGUUA CAAAGUGA GUCCCCUAA@LB@3'-UUU...UUCUG U AGCAA AGGUA...GCA-5'@LB@ \| \|@LB@ 73 37@LB@@LB@@LB@Energy -14.50 kcal/mol@LB@Hybridization Energy -32.397 kcal/mol@LB@Unfolding Energy - mRNA 13.138 kcal/mol@LB@Unfolding Energy - sRNA 4.76382 kcal/mol@LB@@LB@Position - mRNA 239 -- 282@LB@Position - sRNA 38 -- 72@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 38 -- 44@LB@
98	0.004518	0.1538	b2193	narP	-14.47	0.028569	155 -- 204	31 -- 74	response regulator in two-component regulatory system with NarQ	_____________154________________________________________________205\n_____________\|__________________________________________________\|\n5'-UUG...CCAAC_______UCAA___UAA______UAAUAAAAC______A__CUA______CUGAA...AAG-3'\n______________GCUACGC____ACA___UGAUUC_________CUCAGG_GA___CUAUGC\n______________:\|\|\|\|:\|____\|\|\|___::\|\|\|\|_________\|\|\|\|\|\|_\|\|___\|:\|\|\|\|\n______________UGAUGUG____UGU___GUUAAG_________GAGUCC_CU___GGUACG\n3'-UUU...GUUUC______________C________CAACAAAGU______C__AAA______AAUAU...GCA-5'\n_____________\|__________________________________________________\|\n_____________75_________________________________________________30\n	155 -- 161	68 -- 74	-27.903 kcal/mol	6.17297 kcal/mol	7.26183 kcal/mol	154 205@LB@ \| \|@LB@5'-UUG...CCAAC UCAA UAA UAAUAAAAC A CUA CUGAA...AAG-3'@LB@ GCUACGC ACA UGAUUC CUCAGG GA CUAUGC@LB@ :\|\|\|\|:\| \|\|\| ::\|\|\|\| \|\|\|\|\|\| \|\| \|:\|\|\|\|@LB@ UGAUGUG UGU GUUAAG GAGUCC CU GGUACG@LB@3'-UUU...GUUUC C CAACAAAGU C AAA AAUAU...GCA-5'@LB@ \| \|@LB@ 75 30@LB@@LB@@LB@Energy -14.47 kcal/mol@LB@Hybridization Energy -27.903 kcal/mol@LB@Unfolding Energy - mRNA 6.17297 kcal/mol@LB@Unfolding Energy - sRNA 7.26183 kcal/mol@LB@@LB@Position - mRNA 155 -- 204@LB@Position - sRNA 31 -- 74@LB@Position Seed - mRNA 155 -- 161@LB@Position Seed - sRNA 68 -- 74@LB@
153	0.007486	0.1668	b1732	katE	-14.34	0.030774	245 -- 275	42 -- 74	catalase HPII heme d-containing	_____________244___________________________________276\n_____________\|_____________________________________\|\n5'-UGG...UCACC________AUUC______AG__AA_____________AUGGA...ACG-3'\n______________ACUACACG____CAGCGA__CG_______AC_CGGGG\n______________\|\|\|\|\|\|\|:____\|\|\|\|:\|__\|\|_______\|\|_\|:\|\|\|\n______________UGAUGUGU____GUCGUU__GC_______UG_GUCCC\n3'-UUU...GUUUC__________________AA__AACAAAG__A_____CUAAA...GCA-5'\n_____________\|_____________________________________\|\n_____________75____________________________________41\n	246 -- 252	67 -- 73	-24.7059 kcal/mol	5.60497 kcal/mol	4.7632 kcal/mol	244 276@LB@ \| \|@LB@5'-UGG...UCACC AUUC AG AA AUGGA...ACG-3'@LB@ ACUACACG CAGCGA CG AC CGGGG@LB@ \|\|\|\|\|\|\|: \|\|\|\|:\| \|\| \|\| \|:\|\|\|@LB@ UGAUGUGU GUCGUU GC UG GUCCC@LB@3'-UUU...GUUUC AA AACAAAG A CUAAA...GCA-5'@LB@ \| \|@LB@ 75 41@LB@@LB@@LB@Energy -14.34 kcal/mol@LB@Hybridization Energy -24.7059 kcal/mol@LB@Unfolding Energy - mRNA 5.60497 kcal/mol@LB@Unfolding Energy - sRNA 4.7632 kcal/mol@LB@@LB@Position - mRNA 245 -- 275@LB@Position - sRNA 42 -- 74@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 67 -- 73@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@
181	0.009071	0.1747	b3962	sthA	-14.30	0.031527	83 -- 114	34 -- 76	pyridine nucleotide transhydrogenase soluble	_____________82___________________________________________115\n_____________\|____________________________________________\|\n5'-UAC...GAAAC____AAA___AA_______________________AU__AG___GAUAA...CAG-3'\n______________AGAC___GCA__GGC____________CGCUCAGG__AU__CCA\n______________\|\|\|\|___:\|\|__:\|\|____________\|:\|\|\|\|\|\|__\|\|__\|\|\|\n______________UCUG___UGU__UCG____________GUGAGUCC__UA__GGU\n3'-UUU...CCGUU____AUG___G____UUAAGCAACAAA________CC__AA___ACGAA...GCA-5'\n_____________\|____________________________________________\|\n_____________77___________________________________________33\n	99 -- 105	43 -- 49	-23.8174 kcal/mol	4.70621 kcal/mol	4.816 kcal/mol	82 115@LB@ \| \|@LB@5'-UAC...GAAAC AAA AA AU AG GAUAA...CAG-3'@LB@ AGAC GCA GGC CGCUCAGG AU CCA@LB@ \|\|\|\| :\|\| :\|\| \|:\|\|\|\|\|\| \|\| \|\|\|@LB@ UCUG UGU UCG GUGAGUCC UA GGU@LB@3'-UUU...CCGUU AUG G UUAAGCAACAAA CC AA ACGAA...GCA-5'@LB@ \| \|@LB@ 77 33@LB@@LB@@LB@Energy -14.30 kcal/mol@LB@Hybridization Energy -23.8174 kcal/mol@LB@Unfolding Energy - mRNA 4.70621 kcal/mol@LB@Unfolding Energy - sRNA 4.816 kcal/mol@LB@@LB@Position - mRNA 83 -- 114@LB@Position - sRNA 34 -- 76@LB@Position Seed - mRNA 99 -- 105@LB@Position Seed - sRNA 43 -- 49@LB@
163	0.007762	0.1668	b0394	mak	-14.23	0.032787	242 -- 265	40 -- 75	manno(fructo)kinase	_____________241__________________________________266\n_____________\|____________________________________\|\n5'-GUU...GAAGU________UG______G___________________GCAGU...GUG-3'\n______________GAUUGCAC__GGCGAU_____________CAGGGGA\n______________\|\|:\|:\|\|\|__:\|\|:\|\|_____________\|\|\|\|\|\|\|\n______________CUGAUGUG__UCGUUA_____________GUCCCCU\n3'-UUU...CGUUU________UG______AGCAACAAAGUGA_______AAAGG...GCA-5'\n_____________\|____________________________________\|\n_____________76___________________________________39\n	259 -- 265	40 -- 46	-27.5886 kcal/mol	8.58508 kcal/mol	4.77786 kcal/mol	241 266@LB@ \| \|@LB@5'-GUU...GAAGU UG G GCAGU...GUG-3'@LB@ GAUUGCAC GGCGAU CAGGGGA@LB@ \|\|:\|:\|\|\| :\|\|:\|\| \|\|\|\|\|\|\|@LB@ CUGAUGUG UCGUUA GUCCCCU@LB@3'-UUU...CGUUU UG AGCAACAAAGUGA AAAGG...GCA-5'@LB@ \| \|@LB@ 76 39@LB@@LB@@LB@Energy -14.23 kcal/mol@LB@Hybridization Energy -27.5886 kcal/mol@LB@Unfolding Energy - mRNA 8.58508 kcal/mol@LB@Unfolding Energy - sRNA 4.77786 kcal/mol@LB@@LB@Position - mRNA 242 -- 265@LB@Position - sRNA 40 -- 75@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 40 -- 46@LB@
70	0.002881	0.1417	b4144	yjeI	-14.17	0.033933	177 -- 235	31 -- 99	DUF4156 family lipoprotein	_____________176______________________________________________________________________236\n_____________\|________________________________________________________________________\|\n5'-GCA...CGUCC_________AUU________G__UA______________AA_______________CA______G__G____CGCGC...GCA-3'\n______________AGCUCAUUG______AUGGG_AA__AC_AUGCAC_GUAA__________UACUUAG__GGGAUU_UC_GUGC\n______________\|\|\|:\|\|\|:\|______\|\|\|\|\|_\|\|__\|\|_\|::\|\|\|_\|:\|\|__________:\|\|\|:\|\|__\|\|\|\|\|\|_\|\|_:\|\|\|\n______________UCGGGUAGC______UACCC_UU__UG_UGUGUG_CGUU__________GUGAGUC__CCCUAA_AG_UACG\n_____3'-UUUUUU_________ACCCUC_____G__UC__A______U____AAGCAACAAA__________________G____AAUAU...GCA-5'\n_____________\|________________________________________________________________________\|\n_____________100______________________________________________________________________30\n	213 -- 219	44 -- 50	-46.9384 kcal/mol	12.7048 kcal/mol	20.0691 kcal/mol	176 236@LB@ \| \|@LB@5'-GCA...CGUCC AUU G UA AA CA G G CGCGC...GCA-3'@LB@ AGCUCAUUG AUGGG AA AC AUGCAC GUAA UACUUAG GGGAUU UC GUGC@LB@ \|\|\|:\|\|\|:\| \|\|\|\|\| \|\| \|\| \|::\|\|\| \|:\|\| :\|\|\|:\|\| \|\|\|\|\|\| \|\| :\|\|\|@LB@ UCGGGUAGC UACCC UU UG UGUGUG CGUU GUGAGUC CCCUAA AG UACG@LB@ 3'-UUUUUU ACCCUC G UC A U AAGCAACAAA G AAUAU...GCA-5'@LB@ \| \|@LB@ 100 30@LB@@LB@@LB@Energy -14.17 kcal/mol@LB@Hybridization Energy -46.9384 kcal/mol@LB@Unfolding Energy - mRNA 12.7048 kcal/mol@LB@Unfolding Energy - sRNA 20.0691 kcal/mol@LB@@LB@Position - mRNA 177 -- 235@LB@Position - sRNA 31 -- 99@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 44 -- 50@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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