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
157	0.02703	0.5559	b3221	yhcH	-9.14	0.148013	119 -- 127	77 -- 85	DUF386 family protein cupin superfamily	_____________118_______128\n_____________\|_________\|\n5'-AUC...GGCAU_________AUUUA...AAG-3'\n______________UUCAUGUUG\n______________\|\|\|\|:\|\|\|\|\n______________AAGUGCAAC\n3'-CGC...UUUUC_________CGAAA...AAG-5'\n_____________\|_________\|\n_____________86________76\n	121 -- 127	77 -- 83	-10.7393 kcal/mol	1.16925 kcal/mol	0.427568 kcal/mol	118 128@LB@ \| \|@LB@5'-AUC...GGCAU AUUUA...AAG-3'@LB@ UUCAUGUUG@LB@ \|\|\|\|:\|\|\|\|@LB@ AAGUGCAAC@LB@3'-CGC...UUUUC CGAAA...AAG-5'@LB@ \| \|@LB@ 86 76@LB@@LB@@LB@Energy -9.14 kcal/mol@LB@Hybridization Energy -10.7393 kcal/mol@LB@Unfolding Energy - mRNA 1.16925 kcal/mol@LB@Unfolding Energy - sRNA 0.427568 kcal/mol@LB@@LB@Position - mRNA 119 -- 127@LB@Position - sRNA 77 -- 85@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 77 -- 83@LB@
108	0.0187	0.5385	b1210	hemA	-9.14	0.148366	174 -- 184	75 -- 84	glutamyl tRNA reductase	_____________173_________185\n_____________\|___________\|\n5'-CCU...CCCUA__A________AUUAU...ACA-3'\n______________UC_ACGUUGGU\n______________\|\|_\|\|\|\|\|\|\|:\n______________AG_UGCAACCG\n3'-CGC...UUUCA___________AAAUC...AAG-5'\n_____________\|___________\|\n_____________85__________74\n	178 -- 184	75 -- 81	-12.935 kcal/mol	3.29275 kcal/mol	0.505918 kcal/mol	173 185@LB@ \| \|@LB@5'-CCU...CCCUA A AUUAU...ACA-3'@LB@ UC ACGUUGGU@LB@ \|\| \|\|\|\|\|\|\|:@LB@ AG UGCAACCG@LB@3'-CGC...UUUCA AAAUC...AAG-5'@LB@ \| \|@LB@ 85 74@LB@@LB@@LB@Energy -9.14 kcal/mol@LB@Hybridization Energy -12.935 kcal/mol@LB@Unfolding Energy - mRNA 3.29275 kcal/mol@LB@Unfolding Energy - sRNA 0.505918 kcal/mol@LB@@LB@Position - mRNA 174 -- 184@LB@Position - sRNA 75 -- 84@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 75 -- 81@LB@
128	0.02183	0.5385	b0874	ybjE	-9.13	0.148469	198 -- 230	59 -- 85	putative transporter	_____________197_______________________________231\n_____________\|_________________________________\|\n5'-GGG...GGGUU________UUCUG____GUUAAUC____U____CCCCU...UAA-3'\n______________UUCAUGUU_____GGCU_______AUUC_GGUU\n______________\|\|\|\|:\|\|\|_____\|\|\|\|_______\|\|\|\|_:\|\|\|\n______________AAGUGCAA_____CCGA_______UAAG_UCAA\n3'-CGC...UUUUC_________________AAUCAA_____C____CUCUU...AAG-5'\n_____________\|_________________________________\|\n_____________86________________________________58\n	199 -- 205	78 -- 84	-15.801 kcal/mol	4.95896 kcal/mol	1.70749 kcal/mol	197 231@LB@ \| \|@LB@5'-GGG...GGGUU UUCUG GUUAAUC U CCCCU...UAA-3'@LB@ UUCAUGUU GGCU AUUC GGUU@LB@ \|\|\|\|:\|\|\| \|\|\|\| \|\|\|\| :\|\|\|@LB@ AAGUGCAA CCGA UAAG UCAA@LB@3'-CGC...UUUUC AAUCAA C CUCUU...AAG-5'@LB@ \| \|@LB@ 86 58@LB@@LB@@LB@Energy -9.13 kcal/mol@LB@Hybridization Energy -15.801 kcal/mol@LB@Unfolding Energy - mRNA 4.95896 kcal/mol@LB@Unfolding Energy - sRNA 1.70749 kcal/mol@LB@@LB@Position - mRNA 198 -- 230@LB@Position - sRNA 59 -- 85@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 78 -- 84@LB@
88	0.01545	0.5385	b3009	yghB	-9.13	0.148475	202 -- 216	61 -- 78	general envelope maintenance protein; DedA family inner membrane protein; putative multidrug efflux transporter	_____________201________________217\n_____________\|__________________\|\n5'-UCU...GUCCA_______________A__AUAUC...UUG-3'\n______________UGGCU___GUUAUUC_AG\n______________\|\|\|\|\|___\|\|\|\|\|\|\|_\|\|\n______________ACCGA___CAAUAAG_UC\n3'-CGC...GUGCA_____AAU_______C__AACUC...AAG-5'\n_____________\|__________________\|\n_____________79_________________60\n	207 -- 213	64 -- 70	-14.1767 kcal/mol	4.24529 kcal/mol	0.796888 kcal/mol	201 217@LB@ \| \|@LB@5'-UCU...GUCCA A AUAUC...UUG-3'@LB@ UGGCU GUUAUUC AG@LB@ \|\|\|\|\| \|\|\|\|\|\|\| \|\|@LB@ ACCGA CAAUAAG UC@LB@3'-CGC...GUGCA AAU C AACUC...AAG-5'@LB@ \| \|@LB@ 79 60@LB@@LB@@LB@Energy -9.13 kcal/mol@LB@Hybridization Energy -14.1767 kcal/mol@LB@Unfolding Energy - mRNA 4.24529 kcal/mol@LB@Unfolding Energy - sRNA 0.796888 kcal/mol@LB@@LB@Position - mRNA 202 -- 216@LB@Position - sRNA 61 -- 78@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 64 -- 70@LB@
116	0.01945	0.5385	b1175	minD	-9.10	0.150484	222 -- 240	13 -- 34	inhibitor of FtsZ ring polymerization; chromosome-membrane tethering protein; membrane ATPase of the MinCDEE system	_____________221____________________241\n_____________\|______________________\|\n5'-CUG...UUGUU__________C___________UUGGU...AAA-3'\n______________ACUUC__GGG__AAAGGGGGUG\n______________\|\|\|\|\|__\|\|\|__\|\|\|:\|:\|\|\|\|\n______________UGAAG__CCC__UUUUCUCCAC\n3'-CGC...GUCAC_____UU___AA__________GGCGA...AAG-5'\n_____________\|______________________\|\n_____________35_____________________12\n	234 -- 240	13 -- 19	-19.7427 kcal/mol	7.311 kcal/mol	3.33198 kcal/mol	221 241@LB@ \| \|@LB@5'-CUG...UUGUU C UUGGU...AAA-3'@LB@ ACUUC GGG AAAGGGGGUG@LB@ \|\|\|\|\| \|\|\| \|\|\|:\|:\|\|\|\|@LB@ UGAAG CCC UUUUCUCCAC@LB@3'-CGC...GUCAC UU AA GGCGA...AAG-5'@LB@ \| \|@LB@ 35 12@LB@@LB@@LB@Energy -9.10 kcal/mol@LB@Hybridization Energy -19.7427 kcal/mol@LB@Unfolding Energy - mRNA 7.311 kcal/mol@LB@Unfolding Energy - sRNA 3.33198 kcal/mol@LB@@LB@Position - mRNA 222 -- 240@LB@Position - sRNA 13 -- 34@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 13 -- 19@LB@
104	0.0176	0.5385	b2788	gudX	-9.05	0.153387	171 -- 179	57 -- 65	glucarate dehydratase-related protein substrate unknown	_____________170_______180\n_____________\|_________\|\n5'-CGG...GCGUA_________AACCU...CAU-3'\n______________UCGAGUUGA\n______________\|\|\|\|\|\|\|\|\|\n______________AGCUCAACU\n3'-CGC...CAAUA_________CUUUG...AAG-5'\n_____________\|_________\|\n_____________66________56\n	173 -- 179	57 -- 63	-12.8916 kcal/mol	2.7095 kcal/mol	1.13183 kcal/mol	170 180@LB@ \| \|@LB@5'-CGG...GCGUA AACCU...CAU-3'@LB@ UCGAGUUGA@LB@ \|\|\|\|\|\|\|\|\|@LB@ AGCUCAACU@LB@3'-CGC...CAAUA CUUUG...AAG-5'@LB@ \| \|@LB@ 66 56@LB@@LB@@LB@Energy -9.05 kcal/mol@LB@Hybridization Energy -12.8916 kcal/mol@LB@Unfolding Energy - mRNA 2.7095 kcal/mol@LB@Unfolding Energy - sRNA 1.13183 kcal/mol@LB@@LB@Position - mRNA 171 -- 179@LB@Position - sRNA 57 -- 65@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 57 -- 63@LB@
82	0.01477	0.5385	b3527	yhjJ	-9.01	0.155560	190 -- 221	62 -- 91	putative periplasmic M16 family chaperone	_____________189_______________________________222\n_____________\|_________________________________\|\n5'-CUC...UUGAU___________AUGCAG___ACAAAA_______CUUUU...GGC-3'\n______________CAGGGGUUCAC______GGC_______AUUCGA\n______________\|\|:::\|\|\|\|\|\|______\|\|\|_______\|\|\|\|\|\|\n______________GUUUUCAAGUG______CCG_______UAAGCU\n3'-CGC...UAGGC___________CAA______AAAUCAA______CAACU...AAG-5'\n_____________\|_________________________________\|\n_____________92________________________________61\n	194 -- 200	81 -- 87	-19.9715 kcal/mol	6.94165 kcal/mol	4.01597 kcal/mol	189 222@LB@ \| \|@LB@5'-CUC...UUGAU AUGCAG ACAAAA CUUUU...GGC-3'@LB@ CAGGGGUUCAC GGC AUUCGA@LB@ \|\|:::\|\|\|\|\|\| \|\|\| \|\|\|\|\|\|@LB@ GUUUUCAAGUG CCG UAAGCU@LB@3'-CGC...UAGGC CAA AAAUCAA CAACU...AAG-5'@LB@ \| \|@LB@ 92 61@LB@@LB@@LB@Energy -9.01 kcal/mol@LB@Hybridization Energy -19.9715 kcal/mol@LB@Unfolding Energy - mRNA 6.94165 kcal/mol@LB@Unfolding Energy - sRNA 4.01597 kcal/mol@LB@@LB@Position - mRNA 190 -- 221@LB@Position - sRNA 62 -- 91@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 81 -- 87@LB@
94	0.01616	0.5385	b4217	ytfK	-8.94	0.160287	283 -- 290	75 -- 82	DUF1107 family protein	_____________282______291\n_____________\|________\|\n5'-GAA...CAAGG________GCUUU...AAU-3'\n______________ACGUUGGC\n______________\|\|\|\|\|\|\|\|\n______________UGCAACCG\n3'-CGC...UCAAG________AAAUC...AAG-5'\n_____________\|________\|\n_____________83_______74\n	284 -- 290	75 -- 81	-13.4875 kcal/mol	4.21202 kcal/mol	0.339284 kcal/mol	282 291@LB@ \| \|@LB@5'-GAA...CAAGG GCUUU...AAU-3'@LB@ ACGUUGGC@LB@ \|\|\|\|\|\|\|\|@LB@ UGCAACCG@LB@3'-CGC...UCAAG AAAUC...AAG-5'@LB@ \| \|@LB@ 83 74@LB@@LB@@LB@Energy -8.94 kcal/mol@LB@Hybridization Energy -13.4875 kcal/mol@LB@Unfolding Energy - mRNA 4.21202 kcal/mol@LB@Unfolding Energy - sRNA 0.339284 kcal/mol@LB@@LB@Position - mRNA 283 -- 290@LB@Position - sRNA 75 -- 82@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 75 -- 81@LB@
168	0.0298	0.5559	b0161	degP	-8.84	0.166335	239 -- 253	75 -- 88	serine endoprotease (protease Do) membrane-associated	_____________238_____________254\n_____________\|_______________\|\n5'-AUU...GCUCU_______G_U_____GUUAU...CGA-3'\n______________GAGUUUA_G_UUGGC\n______________:\|\|\|\|:\|_\|_\|\|\|\|\|\n______________UUCAAGU_C_AACCG\n3'-CGC...GCGUU_______G_______AAAUC...AAG-5'\n_____________\|_______________\|\n_____________89______________74\n	239 -- 245	82 -- 88	-14.9204 kcal/mol	5.56475 kcal/mol	0.515884 kcal/mol	238 254@LB@ \| \|@LB@5'-AUU...GCUCU G U GUUAU...CGA-3'@LB@ GAGUUUA G UUGGC@LB@ :\|\|\|\|:\| \| \|\|\|\|\|@LB@ UUCAAGU C AACCG@LB@3'-CGC...GCGUU G AAAUC...AAG-5'@LB@ \| \|@LB@ 89 74@LB@@LB@@LB@Energy -8.84 kcal/mol@LB@Hybridization Energy -14.9204 kcal/mol@LB@Unfolding Energy - mRNA 5.56475 kcal/mol@LB@Unfolding Energy - sRNA 0.515884 kcal/mol@LB@@LB@Position - mRNA 239 -- 253@LB@Position - sRNA 75 -- 88@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 82 -- 88@LB@
93	0.01594	0.5385	b3430	glgC	-8.76	0.171477	231 -- 238	75 -- 82	glucose-1-phosphate adenylyltransferase	_____________230______239\n_____________\|________\|\n5'-CAG...ACUUA________GCGCC...UGA-3'\n______________AUGUUGGC\n______________\|:\|\|\|\|\|\|\n______________UGCAACCG\n3'-CGC...UCAAG________AAAUC...AAG-5'\n_____________\|________\|\n_____________83_______74\n	232 -- 238	75 -- 81	-11.9398 kcal/mol	2.84031 kcal/mol	0.339284 kcal/mol	230 239@LB@ \| \|@LB@5'-CAG...ACUUA GCGCC...UGA-3'@LB@ AUGUUGGC@LB@ \|:\|\|\|\|\|\|@LB@ UGCAACCG@LB@3'-CGC...UCAAG AAAUC...AAG-5'@LB@ \| \|@LB@ 83 74@LB@@LB@@LB@Energy -8.76 kcal/mol@LB@Hybridization Energy -11.9398 kcal/mol@LB@Unfolding Energy - mRNA 2.84031 kcal/mol@LB@Unfolding Energy - sRNA 0.339284 kcal/mol@LB@@LB@Position - mRNA 231 -- 238@LB@Position - sRNA 75 -- 82@LB@Position Seed - mRNA 232 -- 238@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)

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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