Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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
91	0.0156	0.5385	b0881	clpS	-13.09	0.030255	248 -- 265	74 -- 90	regulatory protein for ClpA substrate specificity	_____________247________________266\n_____________\|__________________\|\n5'-GCA...GAAGA___________AC_C___AAAAC...UCA-3'\n______________AAAAGUUCGCG__G_GCU\n______________\|\|\|\|\|\|\|\|:\|\|__\|_\|\|\|\n______________UUUUCAAGUGC__C_CGA\n3'-CGC...AGGCG___________AA_____AAUCA...AAG-5'\n_____________\|__________________\|\n_____________91_________________73\n	252 -- 258	80 -- 86	-16.9257 kcal/mol	3.31752 kcal/mol	0.517587 kcal/mol	247 266@LB@ \| \|@LB@5'-GCA...GAAGA AC C AAAAC...UCA-3'@LB@ AAAAGUUCGCG G GCU@LB@ \|\|\|\|\|\|\|\|:\|\| \| \|\|\|@LB@ UUUUCAAGUGC C CGA@LB@3'-CGC...AGGCG AA AAUCA...AAG-5'@LB@ \| \|@LB@ 91 73@LB@@LB@@LB@Energy -13.09 kcal/mol@LB@Hybridization Energy -16.9257 kcal/mol@LB@Unfolding Energy - mRNA 3.31752 kcal/mol@LB@Unfolding Energy - sRNA 0.517587 kcal/mol@LB@@LB@Position - mRNA 248 -- 265@LB@Position - sRNA 74 -- 90@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 80 -- 86@LB@
39	0.007274	0.5385	b1636	pdxY	-13.08	0.030384	230 -- 254	60 -- 84	pyridoxamine kinase	_____________229_______________________255\n_____________\|_________________________\|\n5'-UAU...CAGUC________U__A____C__G_____AACAG...UCU-3'\n______________UCACGUUG_UU_UGGU_AU_CGGGU\n______________\|\|\|\|\|\|\|\|_:\|_\|:\|\|_\|\|_\|\|:\|\|\n______________AGUGCAAC_GA_AUCA_UA_GCUCA\n3'-CGC...UUUCA________C__A____A__A_____ACUCU...AAG-5'\n_____________\|_________________________\|\n_____________85________________________59\n	231 -- 237	77 -- 83	-19.8659 kcal/mol	5.09201 kcal/mol	1.69371 kcal/mol	229 255@LB@ \| \|@LB@5'-UAU...CAGUC U A C G AACAG...UCU-3'@LB@ UCACGUUG UU UGGU AU CGGGU@LB@ \|\|\|\|\|\|\|\| :\| \|:\|\| \|\| \|\|:\|\|@LB@ AGUGCAAC GA AUCA UA GCUCA@LB@3'-CGC...UUUCA C A A A ACUCU...AAG-5'@LB@ \| \|@LB@ 85 59@LB@@LB@@LB@Energy -13.08 kcal/mol@LB@Hybridization Energy -19.8659 kcal/mol@LB@Unfolding Energy - mRNA 5.09201 kcal/mol@LB@Unfolding Energy - sRNA 1.69371 kcal/mol@LB@@LB@Position - mRNA 230 -- 254@LB@Position - sRNA 60 -- 84@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 77 -- 83@LB@
22	0.004141	0.5385	b0462	acrB	-13.08	0.030428	256 -- 265	75 -- 84	multidrug efflux system protein	_____________255________266\n_____________\|__________\|\n5'-AAG...UAUCA__________AGGGG...CGC-3'\n______________UCAUGUUGGC\n______________\|\|\|:\|\|\|\|\|\|\n______________AGUGCAACCG\n3'-CGC...UUUCA__________AAAUC...AAG-5'\n_____________\|__________\|\n_____________85_________74\n	259 -- 265	75 -- 81	-16.8887 kcal/mol	3.30616 kcal/mol	0.505918 kcal/mol	255 266@LB@ \| \|@LB@5'-AAG...UAUCA AGGGG...CGC-3'@LB@ UCAUGUUGGC@LB@ \|\|\|:\|\|\|\|\|\|@LB@ AGUGCAACCG@LB@3'-CGC...UUUCA AAAUC...AAG-5'@LB@ \| \|@LB@ 85 74@LB@@LB@@LB@Energy -13.08 kcal/mol@LB@Hybridization Energy -16.8887 kcal/mol@LB@Unfolding Energy - mRNA 3.30616 kcal/mol@LB@Unfolding Energy - sRNA 0.505918 kcal/mol@LB@@LB@Position - mRNA 256 -- 265@LB@Position - sRNA 75 -- 84@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 75 -- 81@LB@
172	0.03064	0.5559	b1542	ydfI	-13.08	0.030437	273 -- 290	69 -- 86	putative NAD-dependent D-mannonate oxidoreductase	_____________272________________291\n_____________\|__________________\|\n5'-CUC...GAAUU______UUA_________GCAUU...ACC-3'\n______________GUUCAU___GGCUUUGGU\n______________\|\|\|\|\|:___\|\|\|\|\|\|:\|\|\n______________CAAGUG___CCGAAAUCA\n3'-CGC...GUUUU______CAA_________AUAAG...AAG-5'\n_____________\|__________________\|\n_____________87_________________68\n	284 -- 290	69 -- 75	-19.6529 kcal/mol	6.00837 kcal/mol	0.568509 kcal/mol	272 291@LB@ \| \|@LB@5'-CUC...GAAUU UUA GCAUU...ACC-3'@LB@ GUUCAU GGCUUUGGU@LB@ \|\|\|\|\|: \|\|\|\|\|\|:\|\|@LB@ CAAGUG CCGAAAUCA@LB@3'-CGC...GUUUU CAA AUAAG...AAG-5'@LB@ \| \|@LB@ 87 68@LB@@LB@@LB@Energy -13.08 kcal/mol@LB@Hybridization Energy -19.6529 kcal/mol@LB@Unfolding Energy - mRNA 6.00837 kcal/mol@LB@Unfolding Energy - sRNA 0.568509 kcal/mol@LB@@LB@Position - mRNA 273 -- 290@LB@Position - sRNA 69 -- 86@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 69 -- 75@LB@
137	0.02312	0.5385	b2153	folE	-12.97	0.031813	230 -- 265	52 -- 87	GTP cyclohydrolase I	_____________229___________________________________266\n_____________\|_____________________________________\|\n5'-CUG...GCCCU________AA___G_______CG____GACU______ACCGC...ACG-3'\n______________GGUUCAUG___GC_UUAGUUG__CGAG____GGAAAC\n______________:\|\|\|\|\|:\|___\|\|_\|\|\|\|\|\|:__\|\|\|\|____:\|\|\|\|\|\n______________UCAAGUGC___CG_AAUCAAU__GCUC____UCUUUG\n3'-CGC...CGUUU________AAC__A_______AA____AAC_______AGAGC...AAG-5'\n_____________\|_____________________________________\|\n_____________88____________________________________51\n	243 -- 249	67 -- 73	-29.7116 kcal/mol	12.3362 kcal/mol	4.40736 kcal/mol	229 266@LB@ \| \|@LB@5'-CUG...GCCCU AA G CG GACU ACCGC...ACG-3'@LB@ GGUUCAUG GC UUAGUUG CGAG GGAAAC@LB@ :\|\|\|\|\|:\| \|\| \|\|\|\|\|\|: \|\|\|\| :\|\|\|\|\|@LB@ UCAAGUGC CG AAUCAAU GCUC UCUUUG@LB@3'-CGC...CGUUU AAC A AA AAC AGAGC...AAG-5'@LB@ \| \|@LB@ 88 51@LB@@LB@@LB@Energy -12.97 kcal/mol@LB@Hybridization Energy -29.7116 kcal/mol@LB@Unfolding Energy - mRNA 12.3362 kcal/mol@LB@Unfolding Energy - sRNA 4.40736 kcal/mol@LB@@LB@Position - mRNA 230 -- 265@LB@Position - sRNA 52 -- 87@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 67 -- 73@LB@
28	0.005203	0.5385	b3308	rplE	-12.95	0.031988	121 -- 134	62 -- 77	50S ribosomal subunit protein L5	_____________120______________135\n_____________\|________________\|\n5'-AAA...GUGUA________________AGACG...AGA-3'\n______________GGCUUUAG__AUUCGA\n______________\|\|\|\|\|\|\|\|__\|\|\|\|\|\|\n______________CCGAAAUC__UAAGCU\n3'-CGC...UGCAA________AA______CAACU...AAG-5'\n_____________\|________________\|\n_____________78_______________61\n	122 -- 128	70 -- 76	-17.2589 kcal/mol	3.56808 kcal/mol	0.736118 kcal/mol	120 135@LB@ \| \|@LB@5'-AAA...GUGUA AGACG...AGA-3'@LB@ GGCUUUAG AUUCGA@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ CCGAAAUC UAAGCU@LB@3'-CGC...UGCAA AA CAACU...AAG-5'@LB@ \| \|@LB@ 78 61@LB@@LB@@LB@Energy -12.95 kcal/mol@LB@Hybridization Energy -17.2589 kcal/mol@LB@Unfolding Energy - mRNA 3.56808 kcal/mol@LB@Unfolding Energy - sRNA 0.736118 kcal/mol@LB@@LB@Position - mRNA 121 -- 134@LB@Position - sRNA 62 -- 77@LB@Position Seed - mRNA 122 -- 128@LB@Position Seed - sRNA 70 -- 76@LB@
177	0.03112	0.5559	b0080	cra	-12.94	0.032158	57 -- 78	62 -- 84	transcriptional repressor-activator for carbon metabolism	_____________56_______________________79\n_____________\|________________________\|\n5'-GGC...ACAUG_________G____UU________AAUCA...AAA-3'\n______________UCACGUUGG_CUUU__UUG__CGA\n______________\|\|\|\|\|\|\|\|\|_\|\|\|\|__\|\|:__\|\|\|\n______________AGUGCAACC_GAAA__AAU__GCU\n3'-CGC...UUUCA______________UC___AA___CAACU...AAG-5'\n_____________\|________________________\|\n_____________85_______________________61\n	59 -- 65	76 -- 82	-19.2849 kcal/mol	4.65103 kcal/mol	1.6921 kcal/mol	56 79@LB@ \| \|@LB@5'-GGC...ACAUG G UU AAUCA...AAA-3'@LB@ UCACGUUGG CUUU UUG CGA@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\| \|\|: \|\|\|@LB@ AGUGCAACC GAAA AAU GCU@LB@3'-CGC...UUUCA UC AA CAACU...AAG-5'@LB@ \| \|@LB@ 85 61@LB@@LB@@LB@Energy -12.94 kcal/mol@LB@Hybridization Energy -19.2849 kcal/mol@LB@Unfolding Energy - mRNA 4.65103 kcal/mol@LB@Unfolding Energy - sRNA 1.6921 kcal/mol@LB@@LB@Position - mRNA 57 -- 78@LB@Position - sRNA 62 -- 84@LB@Position Seed - mRNA 59 -- 65@LB@Position Seed - sRNA 76 -- 82@LB@
122	0.02068	0.5385	b4529	ydbJ	-12.93	0.032363	174 -- 233	8 -- 79	DUF333 family putative lipoprotein	_____________173_______________________________________________________________________234\n_____________\|_________________________________________________________________________\|\n5'-GCA...GUCGU_______GAA________UCA______GAAAA__U___A____C____________________U________UUAUU...GUU-3'\n______________UUGGCUU_________GA___GAGGAA_____GA_GCG_GCAG_G_UUUU__GGGU____AGGG_GUGCCGCU\n______________\|\|\|\|\|\|\|_________\|\|___\|\|\|:\|\|_____\|\|_:\|\|_\|\|\|\|_\|_:\|\|:__\|\|\|\|____\|\|:\|_\|\|\|\|\|\|\|\|\n______________AACCGAA_________CU___CUCUUU_____CU_UGC_CGUC_C_GAAG__CCCA____UCUC_CACGGCGA\n3'-CGC...AGUGC_______AUCAAUAAG__CAA______GAGAG__U___C____A_U____UU____AUUU_____________GGCAAAG-5'\n_____________\|_________________________________________________________________________\|\n_____________80________________________________________________________________________7\n	227 -- 233	8 -- 14	-51.0346 kcal/mol	16.597 kcal/mol	21.5113 kcal/mol	173 234@LB@ \| \|@LB@5'-GCA...GUCGU GAA UCA GAAAA U A C U UUAUU...GUU-3'@LB@ UUGGCUU GA GAGGAA GA GCG GCAG G UUUU GGGU AGGG GUGCCGCU@LB@ \|\|\|\|\|\|\| \|\| \|\|\|:\|\| \|\| :\|\| \|\|\|\| \| :\|\|: \|\|\|\| \|\|:\| \|\|\|\|\|\|\|\|@LB@ AACCGAA CU CUCUUU CU UGC CGUC C GAAG CCCA UCUC CACGGCGA@LB@3'-CGC...AGUGC AUCAAUAAG CAA GAGAG U C A U UU AUUU GGCAAAG-5'@LB@ \| \|@LB@ 80 7@LB@@LB@@LB@Energy -12.93 kcal/mol@LB@Hybridization Energy -51.0346 kcal/mol@LB@Unfolding Energy - mRNA 16.597 kcal/mol@LB@Unfolding Energy - sRNA 21.5113 kcal/mol@LB@@LB@Position - mRNA 174 -- 233@LB@Position - sRNA 8 -- 79@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 8 -- 14@LB@
53	0.01075	0.5385	b2215	ompC	-12.88	0.032936	67 -- 90	57 -- 76	outer membrane porin protein C	_____________66_______________________91\n_____________\|________________________\|\n5'-AUC...UAAAA________AUCA______U_____AUUAU...AUC-3'\n______________GUUUUAGU____UAUUCG_GUUGG\n______________\|:\|\|\|\|\|\|____\|\|\|\|\|\|_\|\|\|\|:\n______________CGAAAUCA____AUAAGC_CAACU\n3'-CGC...GCAAC__________________U_____CUUUG...AAG-5'\n_____________\|________________________\|\n_____________77_______________________56\n	68 -- 74	69 -- 75	-17.5321 kcal/mol	3.43109 kcal/mol	1.21756 kcal/mol	66 91@LB@ \| \|@LB@5'-AUC...UAAAA AUCA U AUUAU...AUC-3'@LB@ GUUUUAGU UAUUCG GUUGG@LB@ \|:\|\|\|\|\|\| \|\|\|\|\|\| \|\|\|\|:@LB@ CGAAAUCA AUAAGC CAACU@LB@3'-CGC...GCAAC U CUUUG...AAG-5'@LB@ \| \|@LB@ 77 56@LB@@LB@@LB@Energy -12.88 kcal/mol@LB@Hybridization Energy -17.5321 kcal/mol@LB@Unfolding Energy - mRNA 3.43109 kcal/mol@LB@Unfolding Energy - sRNA 1.21756 kcal/mol@LB@@LB@Position - mRNA 67 -- 90@LB@Position - sRNA 57 -- 76@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 69 -- 75@LB@
68	0.013	0.5385	b2823	ppdC	-12.74	0.034901	243 -- 262	69 -- 89	putative prepilin peptidase-dependent protein	_____________242___________________263\n_____________\|_____________________\|\n5'-ACG...UGCCG_____A_________GA____GUUGA...UCC-3'\n______________GAGGU__AUGUUGGC__UGGU\n______________:\|:\|\|__\|:\|\|\|\|\|\|__\|:\|\|\n______________UUUCA__UGCAACCG__AUCA\n3'-CGC...GGCGU_____AG________AA____AUAAG...AAG-5'\n_____________\|_____________________\|\n_____________90____________________68\n	250 -- 256	75 -- 81	-18.5568 kcal/mol	5.24273 kcal/mol	0.572143 kcal/mol	242 263@LB@ \| \|@LB@5'-ACG...UGCCG A GA GUUGA...UCC-3'@LB@ GAGGU AUGUUGGC UGGU@LB@ :\|:\|\| \|:\|\|\|\|\|\| \|:\|\|@LB@ UUUCA UGCAACCG AUCA@LB@3'-CGC...GGCGU AG AA AUAAG...AAG-5'@LB@ \| \|@LB@ 90 68@LB@@LB@@LB@Energy -12.74 kcal/mol@LB@Hybridization Energy -18.5568 kcal/mol@LB@Unfolding Energy - mRNA 5.24273 kcal/mol@LB@Unfolding Energy - sRNA 0.572143 kcal/mol@LB@@LB@Position - mRNA 243 -- 262@LB@Position - sRNA 69 -- 89@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 75 -- 81@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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