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
97	0.004509	0.1538	b0465	mscK	-15.00	0.020897	217 -- 248	49 -- 74	mechanosensitive channel protein intermediate conductance K+ regulated	_____________216______________________________249\n_____________\|________________________________\|\n5'-CGA...CCAGU______AACGAU_______U______U_____GCAUU...CGC-3'\n______________AUUACA______CACGGCA_UUUGUU_UUUCA\n______________\|:\|\|\|\|______\|\|\|:\|\|\|_\|\|:\|\|\|_\|\|\|\|\|\n______________UGAUGU______GUGUCGU_AAGCAA_AAAGU\n3'-UUU...GUUUC___________________U______C_____GAGUC...GCA-5'\n_____________\|________________________________\|\n_____________75_______________________________48\n	229 -- 235	62 -- 68	-21.8954 kcal/mol	3.22234 kcal/mol	3.67122 kcal/mol	216 249@LB@ \| \|@LB@5'-CGA...CCAGU AACGAU U U GCAUU...CGC-3'@LB@ AUUACA CACGGCA UUUGUU UUUCA@LB@ \|:\|\|\|\| \|\|\|:\|\|\| \|\|:\|\|\| \|\|\|\|\|@LB@ UGAUGU GUGUCGU AAGCAA AAAGU@LB@3'-UUU...GUUUC U C GAGUC...GCA-5'@LB@ \| \|@LB@ 75 48@LB@@LB@@LB@Energy -15.00 kcal/mol@LB@Hybridization Energy -21.8954 kcal/mol@LB@Unfolding Energy - mRNA 3.22234 kcal/mol@LB@Unfolding Energy - sRNA 3.67122 kcal/mol@LB@@LB@Position - mRNA 217 -- 248@LB@Position - sRNA 49 -- 74@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 62 -- 68@LB@
74	0.003066	0.1452	b0467	priC	-11.71	0.118543	157 -- 193	43 -- 75	primosomal replication protein N''	_____________156___________________________________194\n_____________\|_____________________________________\|\n5'-GGG...AGAGU______UUUA_____A_____AUCAU_______G___UCUUA...GUU-3'\n______________GGCUAC____GCAUA_CAAUU_____UUUCAUU_AGG\n______________\|:\|\|\|\|____:\|\|:\|_\|\|\|\|\|_____\|\|\|\|\|:\|_\|\|\|\n______________CUGAUG____UGUGU_GUUAA_____AAAGUGA_UCC\n3'-UUU...CGUUU_______________C_____GCAAC_______G___CCUAA...GCA-5'\n_____________\|_____________________________________\|\n_____________76____________________________________42\n	183 -- 189	47 -- 53	-24.815 kcal/mol	8.75149 kcal/mol	4.35266 kcal/mol	156 194@LB@ \| \|@LB@5'-GGG...AGAGU UUUA A AUCAU G UCUUA...GUU-3'@LB@ GGCUAC GCAUA CAAUU UUUCAUU AGG@LB@ \|:\|\|\|\| :\|\|:\| \|\|\|\|\| \|\|\|\|\|:\| \|\|\|@LB@ CUGAUG UGUGU GUUAA AAAGUGA UCC@LB@3'-UUU...CGUUU C GCAAC G CCUAA...GCA-5'@LB@ \| \|@LB@ 76 42@LB@@LB@@LB@Energy -11.71 kcal/mol@LB@Hybridization Energy -24.815 kcal/mol@LB@Unfolding Energy - mRNA 8.75149 kcal/mol@LB@Unfolding Energy - sRNA 4.35266 kcal/mol@LB@@LB@Position - mRNA 157 -- 193@LB@Position - sRNA 43 -- 75@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 47 -- 53@LB@
73	0.00298	0.1437	b0474	adk	-13.48	0.049381	180 -- 198	34 -- 50	adenylate kinase	_____________179_________________199\n_____________\|___________________\|\n5'-ACC...CGACA_____UA____________CAAUG...AUA-3'\n______________CAUUU__AGGGGAUUUUCG\n______________\|\|:\|:__\|\|\|\|\|\|\|\|\|:\|:\n______________GUGAG__UCCCCUAAAGGU\n3'-UUU...ACAAA___________________ACGAA...GCA-5'\n_____________\|___________________\|\n_____________51__________________33\n	191 -- 197	35 -- 41	-19.9961 kcal/mol	4.64453 kcal/mol	1.87382 kcal/mol	179 199@LB@ \| \|@LB@5'-ACC...CGACA UA CAAUG...AUA-3'@LB@ CAUUU AGGGGAUUUUCG@LB@ \|\|:\|: \|\|\|\|\|\|\|\|\|:\|:@LB@ GUGAG UCCCCUAAAGGU@LB@3'-UUU...ACAAA ACGAA...GCA-5'@LB@ \| \|@LB@ 51 33@LB@@LB@@LB@Energy -13.48 kcal/mol@LB@Hybridization Energy -19.9961 kcal/mol@LB@Unfolding Energy - mRNA 4.64453 kcal/mol@LB@Unfolding Energy - sRNA 1.87382 kcal/mol@LB@@LB@Position - mRNA 180 -- 198@LB@Position - sRNA 34 -- 50@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 35 -- 41@LB@
6	1.32e-05	0.00774	b0475	hemH	-21.46	0.000115	123 -- 162	34 -- 75	ferrochelatase	_____________122__________________________________________163\n_____________\|____________________________________________\|\n5'-CGG...GAUUU___CU_U__________A___CUUC________CU_________CUACA...GCG-3'\n______________GAC__C_CACAGCAAUU_GUU____UUC_CUCA_____UUUCCG\n______________\|\|\|__\|_\|\|\|\|\|\|\|\|\|\|_\|\|\|____\|\|\|_\|\|\|\|_____\|\|\|\|\|:\n______________CUG__G_GUGUCGUUAA_CAA____AAG_GAGU_____AAAGGU\n3'-UUU...CGUUU___AU_U__________G___CA_____U____CCCCU______ACGAA...GCA-5'\n_____________\|____________________________________________\|\n_____________76___________________________________________33\n	133 -- 139	59 -- 65	-29.8744 kcal/mol	3.60304 kcal/mol	4.816 kcal/mol	122 163@LB@ \| \|@LB@5'-CGG...GAUUU CU U A CUUC CU CUACA...GCG-3'@LB@ GAC C CACAGCAAUU GUU UUC CUCA UUUCCG@LB@ \|\|\| \| \|\|\|\|\|\|\|\|\|\| \|\|\| \|\|\| \|\|\|\| \|\|\|\|\|:@LB@ CUG G GUGUCGUUAA CAA AAG GAGU AAAGGU@LB@3'-UUU...CGUUU AU U G CA U CCCCU ACGAA...GCA-5'@LB@ \| \|@LB@ 76 33@LB@@LB@@LB@Energy -21.46 kcal/mol@LB@Hybridization Energy -29.8744 kcal/mol@LB@Unfolding Energy - mRNA 3.60304 kcal/mol@LB@Unfolding Energy - sRNA 4.816 kcal/mol@LB@@LB@Position - mRNA 123 -- 162@LB@Position - sRNA 34 -- 75@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 59 -- 65@LB@
118	0.005291	0.1553	b0481	ybaK	-9.02	0.349126	203 -- 225	45 -- 75	Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase	_____________202_____________________________226\n_____________\|_______________________________\|\n5'-AAU...ACCAU______C______UAAA______________AAAAA...UCG-3'\n______________GAC_AC_CGCAGU___________UUACUCG\n______________\|\|\|_\|\|_\|:\|\|\|:___________\|:\|\|\|\|:\n______________CUG_UG_GUGUCG___________AGUGAGU\n3'-UUU...CGUUU___A__U______UUAAGCAACAA_______CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	219 -- 225	45 -- 51	-15.8984 kcal/mol	3.13427 kcal/mol	3.74078 kcal/mol	202 226@LB@ \| \|@LB@5'-AAU...ACCAU C UAAA AAAAA...UCG-3'@LB@ GAC AC CGCAGU UUACUCG@LB@ \|\|\| \|\| \|:\|\|\|: \|:\|\|\|\|:@LB@ CUG UG GUGUCG AGUGAGU@LB@3'-UUU...CGUUU A U UUAAGCAACAA CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -9.02 kcal/mol@LB@Hybridization Energy -15.8984 kcal/mol@LB@Unfolding Energy - mRNA 3.13427 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 203 -- 225@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 45 -- 51@LB@
120	0.005393	0.1553	b0523	purE	-13.83	0.040764	102 -- 146	30 -- 75	N5-carboxyaminoimidazole ribonucleotide mutase	_____________101________________________________________________147\n_____________\|__________________________________________________\|\n5'-UGG...UUGCU____U____GC__C____C_____UUCC______UC______________AUUCU...UGA-3'\n______________GAUU_CACA__CA_GCAA__CGUU____UUGCUC______UUUCCGUGCU\n______________\|\|:\|_\|\|\|\|__\|\|_\|\|\|\|__\|\|\|\|____\|::\|\|\|______\|\|\|\|\|:\|\|\|\|\n______________CUGA_GUGU__GU_CGUU__GCAA____AGUGAG______AAAGGUACGA\n3'-UUU...CGUUU____U_____________AA____CAA_______UCCCCU__________AUAUU...GCA-5'\n_____________\|__________________________________________________\|\n_____________76_________________________________________________29\n	140 -- 146	30 -- 36	-29.2897 kcal/mol	7.36654 kcal/mol	8.08958 kcal/mol	101 147@LB@ \| \|@LB@5'-UGG...UUGCU U GC C C UUCC UC AUUCU...UGA-3'@LB@ GAUU CACA CA GCAA CGUU UUGCUC UUUCCGUGCU@LB@ \|\|:\| \|\|\|\| \|\| \|\|\|\| \|\|\|\| \|::\|\|\| \|\|\|\|\|:\|\|\|\|@LB@ CUGA GUGU GU CGUU GCAA AGUGAG AAAGGUACGA@LB@3'-UUU...CGUUU U AA CAA UCCCCU AUAUU...GCA-5'@LB@ \| \|@LB@ 76 29@LB@@LB@@LB@Energy -13.83 kcal/mol@LB@Hybridization Energy -29.2897 kcal/mol@LB@Unfolding Energy - mRNA 7.36654 kcal/mol@LB@Unfolding Energy - sRNA 8.08958 kcal/mol@LB@@LB@Position - mRNA 102 -- 146@LB@Position - sRNA 30 -- 75@LB@Position Seed - mRNA 140 -- 146@LB@Position Seed - sRNA 30 -- 36@LB@
40	0.0008945	0.07693	b0525	ppiB	-7.31	0.578113	284 -- 298	61 -- 76	peptidyl-prolyl cis-trans isomerase B (rotamase B)	_____________283______________299\n_____________\|________________\|\n5'-UGU...UUCCU___________C____AG-3'\n______________GGACUAC_UGC_GCGA\n______________:\|\|\|\|\|\|_::\|_\|\|:\|\n______________UCUGAUG_GUG_CGUU\n3'-UUU...CCGUU_______U___U____AAGCA...GCA-5'\n_____________\|________________\|\n_____________77_______________60\n	284 -- 290	70 -- 76	-14.2171 kcal/mol	3.65067 kcal/mol	3.25604 kcal/mol	283 299@LB@ \| \|@LB@5'-UGU...UUCCU C AG-3'@LB@ GGACUAC UGC GCGA@LB@ :\|\|\|\|\|\| ::\| \|\|:\|@LB@ UCUGAUG GUG CGUU@LB@3'-UUU...CCGUU U U AAGCA...GCA-5'@LB@ \| \|@LB@ 77 60@LB@@LB@@LB@Energy -7.31 kcal/mol@LB@Hybridization Energy -14.2171 kcal/mol@LB@Unfolding Energy - mRNA 3.65067 kcal/mol@LB@Unfolding Energy - sRNA 3.25604 kcal/mol@LB@@LB@Position - mRNA 284 -- 298@LB@Position - sRNA 61 -- 76@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 70 -- 76@LB@
53	0.001859	0.1218	b0529	folD	-11.41	0.136116	200 -- 226	61 -- 85	bifunctional 5 10-methylene-tetrahydrofolate dehydrogenase/ 5 10-methylene-tetrahydrofolate cyclohydrolase	_____________199_________________________227\n_____________\|___________________________\|\n5'-CAA...UCUCU_____CA___________UG_______AACGA...CAC-3'\n______________GAUGG__GCAAAGAUUAU__ACGGUAA\n______________\|\|\|\|\|__\|\|\|\|\|\|\|:\|\|:__\|\|:\|:\|\|\n______________CUACC__CGUUUCUGAUG__UGUCGUU\n3'-UUU...ACCCU__________________UG_______AAGCA...GCA-5'\n_____________\|___________________________\|\n_____________86__________________________60\n	220 -- 226	61 -- 67	-27.4215 kcal/mol	5.77154 kcal/mol	10.2439 kcal/mol	199 227@LB@ \| \|@LB@5'-CAA...UCUCU CA UG AACGA...CAC-3'@LB@ GAUGG GCAAAGAUUAU ACGGUAA@LB@ \|\|\|\|\| \|\|\|\|\|\|\|:\|\|: \|\|:\|:\|\|@LB@ CUACC CGUUUCUGAUG UGUCGUU@LB@3'-UUU...ACCCU UG AAGCA...GCA-5'@LB@ \| \|@LB@ 86 60@LB@@LB@@LB@Energy -11.41 kcal/mol@LB@Hybridization Energy -27.4215 kcal/mol@LB@Unfolding Energy - mRNA 5.77154 kcal/mol@LB@Unfolding Energy - sRNA 10.2439 kcal/mol@LB@@LB@Position - mRNA 200 -- 226@LB@Position - sRNA 61 -- 85@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 61 -- 67@LB@
65	0.002677	0.1417	b0584	fepA	-11.47	0.132508	209 -- 249	37 -- 78	ferrienterobactin outer membrane transporter	_____________208___________________________________________250\n_____________\|_____________________________________________\|\n5'-GAA...AACAA___________U_CCU___C________G____A__U________AUGGG...ACG-3'\n______________GAAGAUU_CAU_C___GGC___UUGUUG__UCA_UC_GGGGAUUU\n______________:\|\|\|\|:\|_\|\|:_\|___:\|\|___\|:\|\|\|\|__\|\|\|_\|\|_\|\|\|\|\|\|\|\|\n______________UUUCUGA_GUG_G___UCG___AGCAAC__AGU_AG_CCCCUAAA\n3'-UUU...ACCCG_______U___U_______UUA______AA___G__U________GGUAC...GCA-5'\n_____________\|_____________________________________________\|\n_____________79____________________________________________36\n	243 -- 249	37 -- 43	-30.6633 kcal/mol	14.4176 kcal/mol	4.77973 kcal/mol	208 250@LB@ \| \|@LB@5'-GAA...AACAA U CCU C G A U AUGGG...ACG-3'@LB@ GAAGAUU CAU C GGC UUGUUG UCA UC GGGGAUUU@LB@ :\|\|\|\|:\| \|\|: \| :\|\| \|:\|\|\|\| \|\|\| \|\| \|\|\|\|\|\|\|\|@LB@ UUUCUGA GUG G UCG AGCAAC AGU AG CCCCUAAA@LB@3'-UUU...ACCCG U U UUA AA G U GGUAC...GCA-5'@LB@ \| \|@LB@ 79 36@LB@@LB@@LB@Energy -11.47 kcal/mol@LB@Hybridization Energy -30.6633 kcal/mol@LB@Unfolding Energy - mRNA 14.4176 kcal/mol@LB@Unfolding Energy - sRNA 4.77973 kcal/mol@LB@@LB@Position - mRNA 209 -- 249@LB@Position - sRNA 37 -- 78@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 37 -- 43@LB@
152	0.007399	0.1668	b0591	entS	-13.87	0.039944	258 -- 287	45 -- 70	enterobactin exporter iron-regulated	_____________257____________________________288\n_____________\|______________________________\|\n5'-AAU...CGUUU_________UUCC___CUC______U____AUUGU...UGG-3'\n______________CGCGCAGUA____UCG___GUUUCA_CUCA\n______________\|:\|:\|\|\|:\|____\|\|\|___\|\|\|\|\|\|_\|\|\|\|\n______________GUGUGUCGU____AGC___CAAAGU_GAGU\n3'-UUU...CUGAU_________UA_____AA____________CCCCU...GCA-5'\n_____________\|______________________________\|\n_____________71_____________________________44\n	260 -- 266	62 -- 68	-23.1768 kcal/mol	5.59312 kcal/mol	3.71317 kcal/mol	257 288@LB@ \| \|@LB@5'-AAU...CGUUU UUCC CUC U AUUGU...UGG-3'@LB@ CGCGCAGUA UCG GUUUCA CUCA@LB@ \|:\|:\|\|\|:\| \|\|\| \|\|\|\|\|\| \|\|\|\|@LB@ GUGUGUCGU AGC CAAAGU GAGU@LB@3'-UUU...CUGAU UA AA CCCCU...GCA-5'@LB@ \| \|@LB@ 71 44@LB@@LB@@LB@Energy -13.87 kcal/mol@LB@Hybridization Energy -23.1768 kcal/mol@LB@Unfolding Energy - mRNA 5.59312 kcal/mol@LB@Unfolding Energy - sRNA 3.71317 kcal/mol@LB@@LB@Position - mRNA 258 -- 287@LB@Position - sRNA 45 -- 70@LB@Position Seed - mRNA 260 -- 266@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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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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