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
14	0.002739	0.5385	b0903	pflB	-11.82	0.050867	80 -- 105	57 -- 81	formate C-acetyltransferase 1 anaerobic; pyruvate formate-lyase 1	_____________79_________________________106\n_____________\|__________________________\|\n5'-CAC...AUUAU__G____GGUUU____G_________CAUAC...ACU-3'\n______________CG_UGGU_____GUUG_UUGGGUUGA\n______________\|\|_\|\|\|:_____\|\|\|:_\|:\|:\|\|\|\|\|\n______________GC_ACCG_____CAAU_AGCUCAACU\n3'-CGC...CAAGU__A____AAAU_____A_________CUUUG...AAG-5'\n_____________\|__________________________\|\n_____________82_________________________56\n	99 -- 105	57 -- 63	-19.5015 kcal/mol	6.38537 kcal/mol	1.29708 kcal/mol	79 106@LB@ \| \|@LB@5'-CAC...AUUAU G GGUUU G CAUAC...ACU-3'@LB@ CG UGGU GUUG UUGGGUUGA@LB@ \|\| \|\|\|: \|\|\|: \|:\|:\|\|\|\|\|@LB@ GC ACCG CAAU AGCUCAACU@LB@3'-CGC...CAAGU A AAAU A CUUUG...AAG-5'@LB@ \| \|@LB@ 82 56@LB@@LB@@LB@Energy -11.82 kcal/mol@LB@Hybridization Energy -19.5015 kcal/mol@LB@Unfolding Energy - mRNA 6.38537 kcal/mol@LB@Unfolding Energy - sRNA 1.29708 kcal/mol@LB@@LB@Position - mRNA 80 -- 105@LB@Position - sRNA 57 -- 81@LB@Position Seed - mRNA 99 -- 105@LB@Position Seed - sRNA 57 -- 63@LB@
131	0.02244	0.5385	b1713	pheT	-10.81	0.076409	64 -- 80	73 -- 89	phenylalanine tRNA synthetase beta subunit	_____________63________________81\n_____________\|_________________\|\n5'-CUG...ACCCG_________UC______CGCCU...ACG-3'\n______________GAAGUUUAC__UGGUUU\n______________:\|\|\|\|\|:\|\|__\|\|\|:\|\|\n______________UUUCAAGUG__ACCGAA\n3'-CGC...GGCGU_________CA______AUCAA...AAG-5'\n_____________\|_________________\|\n_____________90________________72\n	66 -- 72	81 -- 87	-14.6363 kcal/mol	3.30516 kcal/mol	0.517627 kcal/mol	63 81@LB@ \| \|@LB@5'-CUG...ACCCG UC CGCCU...ACG-3'@LB@ GAAGUUUAC UGGUUU@LB@ :\|\|\|\|\|:\|\| \|\|\|:\|\|@LB@ UUUCAAGUG ACCGAA@LB@3'-CGC...GGCGU CA AUCAA...AAG-5'@LB@ \| \|@LB@ 90 72@LB@@LB@@LB@Energy -10.81 kcal/mol@LB@Hybridization Energy -14.6363 kcal/mol@LB@Unfolding Energy - mRNA 3.30516 kcal/mol@LB@Unfolding Energy - sRNA 0.517627 kcal/mol@LB@@LB@Position - mRNA 64 -- 80@LB@Position - sRNA 73 -- 89@LB@Position Seed - mRNA 66 -- 72@LB@Position Seed - sRNA 81 -- 87@LB@
151	0.02561	0.5485	b4041	plsB	-9.39	0.134646	197 -- 210	74 -- 86	glycerol-3-phosphate O-acyltransferase	_____________196____________211\n_____________\|______________\|\n5'-UCG...ACAUC________CC____GGCCA...UGG-3'\n______________GUUUAUGU__GGCU\n______________\|\|\|:\|:\|\|__\|\|\|\|\n______________CAAGUGCA__CCGA\n3'-CGC...GUUUU________A_____AAUCA...AAG-5'\n_____________\|______________\|\n_____________87_____________73\n	198 -- 204	79 -- 85	-13.0466 kcal/mol	3.14742 kcal/mol	0.513318 kcal/mol	196 211@LB@ \| \|@LB@5'-UCG...ACAUC CC GGCCA...UGG-3'@LB@ GUUUAUGU GGCU@LB@ \|\|\|:\|:\|\| \|\|\|\|@LB@ CAAGUGCA CCGA@LB@3'-CGC...GUUUU A AAUCA...AAG-5'@LB@ \| \|@LB@ 87 73@LB@@LB@@LB@Energy -9.39 kcal/mol@LB@Hybridization Energy -13.0466 kcal/mol@LB@Unfolding Energy - mRNA 3.14742 kcal/mol@LB@Unfolding Energy - sRNA 0.513318 kcal/mol@LB@@LB@Position - mRNA 197 -- 210@LB@Position - sRNA 74 -- 86@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 79 -- 85@LB@
51	0.01052	0.5385	b0751	pnuC	-11.84	0.050492	77 -- 89	77 -- 89	nicotinamide riboside transporter	_____________76____________90\n_____________\|_____________\|\n5'-CGC...AUCAC_____________AUGAA...GGU-3'\n______________GAGGUUCAUGUUG\n______________:\|:\|\|\|\|\|:\|\|\|\|\n______________UUUCAAGUGCAAC\n3'-CGC...GGCGU_____________CGAAA...AAG-5'\n_____________\|_____________\|\n_____________90____________76\n	83 -- 89	77 -- 83	-16.9239 kcal/mol	4.57656 kcal/mol	0.510111 kcal/mol	76 90@LB@ \| \|@LB@5'-CGC...AUCAC AUGAA...GGU-3'@LB@ GAGGUUCAUGUUG@LB@ :\|:\|\|\|\|\|:\|\|\|\|@LB@ UUUCAAGUGCAAC@LB@3'-CGC...GGCGU CGAAA...AAG-5'@LB@ \| \|@LB@ 90 76@LB@@LB@@LB@Energy -11.84 kcal/mol@LB@Hybridization Energy -16.9239 kcal/mol@LB@Unfolding Energy - mRNA 4.57656 kcal/mol@LB@Unfolding Energy - sRNA 0.510111 kcal/mol@LB@@LB@Position - mRNA 77 -- 89@LB@Position - sRNA 77 -- 89@LB@Position Seed - mRNA 83 -- 89@LB@Position Seed - sRNA 77 -- 83@LB@
142	0.02338	0.5385	b1126	potA	-10.56	0.084569	277 -- 295	14 -- 34	spermidine/putrescine ABC transporter ATPase	_____________276___________________296\n_____________\|_____________________\|\n5'-CAA...CAAAU_______U_____________CAUUC-3'\n______________GCUUUGA_GGU__AAAGAGGU\n______________:\|\|\|::\|_\|\|\|__\|\|\|\|\|\|\|\|\n______________UGAAGUU_CCA__UUUCUCCA\n3'-CGC...GUCAC_______C___AU________CGGCG...AAG-5'\n_____________\|_____________________\|\n_____________35____________________13\n	289 -- 295	14 -- 20	-18.1028 kcal/mol	4.21038 kcal/mol	3.33169 kcal/mol	276 296@LB@ \| \|@LB@5'-CAA...CAAAU U CAUUC-3'@LB@ GCUUUGA GGU AAAGAGGU@LB@ :\|\|\|::\| \|\|\| \|\|\|\|\|\|\|\|@LB@ UGAAGUU CCA UUUCUCCA@LB@3'-CGC...GUCAC C AU CGGCG...AAG-5'@LB@ \| \|@LB@ 35 13@LB@@LB@@LB@Energy -10.56 kcal/mol@LB@Hybridization Energy -18.1028 kcal/mol@LB@Unfolding Energy - mRNA 4.21038 kcal/mol@LB@Unfolding Energy - sRNA 3.33169 kcal/mol@LB@@LB@Position - mRNA 277 -- 295@LB@Position - sRNA 14 -- 34@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 14 -- 20@LB@
112	0.0191	0.5385	b0854	potF	-9.27	0.140763	36 -- 50	64 -- 78	putrescine ABC transporter periplasmic binding protein	_____________35______________51\n_____________\|_______________\|\n5'-UAC...AACCC_____AA________UUGCG...ACA-3'\n______________UGGCU__AGUUAUUC\n______________\|\|\|\|\|__\|\|\|\|\|\|\|\|\n______________ACCGA__UCAAUAAG\n3'-CGC...GUGCA_____AA________CUCAA...AAG-5'\n_____________\|_______________\|\n_____________79______________63\n	44 -- 50	64 -- 70	-15.0609 kcal/mol	5.5152 kcal/mol	0.273858 kcal/mol	35 51@LB@ \| \|@LB@5'-UAC...AACCC AA UUGCG...ACA-3'@LB@ UGGCU AGUUAUUC@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ ACCGA UCAAUAAG@LB@3'-CGC...GUGCA AA CUCAA...AAG-5'@LB@ \| \|@LB@ 79 63@LB@@LB@@LB@Energy -9.27 kcal/mol@LB@Hybridization Energy -15.0609 kcal/mol@LB@Unfolding Energy - mRNA 5.5152 kcal/mol@LB@Unfolding Energy - sRNA 0.273858 kcal/mol@LB@@LB@Position - mRNA 36 -- 50@LB@Position - sRNA 64 -- 78@LB@Position Seed - mRNA 44 -- 50@LB@Position Seed - sRNA 64 -- 70@LB@
36	0.006672	0.5385	b3956	ppc	-10.31	0.093393	270 -- 282	76 -- 88	phosphoenolpyruvate carboxylase	_____________269___________283\n_____________\|_____________\|\n5'-CUU...CCAUC___GA________GAGAA...AAC-3'\n______________AAG__UGCGUUGG\n______________\|\|\|__::\|\|\|\|\|\|\n______________UUC__GUGCAACC\n3'-CGC...GCGUU___AA________GAAAU...AAG-5'\n_____________\|_____________\|\n_____________89____________75\n	276 -- 282	76 -- 82	-12.0501 kcal/mol	1.22517 kcal/mol	0.512479 kcal/mol	269 283@LB@ \| \|@LB@5'-CUU...CCAUC GA GAGAA...AAC-3'@LB@ AAG UGCGUUGG@LB@ \|\|\| ::\|\|\|\|\|\|@LB@ UUC GUGCAACC@LB@3'-CGC...GCGUU AA GAAAU...AAG-5'@LB@ \| \|@LB@ 89 75@LB@@LB@@LB@Energy -10.31 kcal/mol@LB@Hybridization Energy -12.0501 kcal/mol@LB@Unfolding Energy - mRNA 1.22517 kcal/mol@LB@Unfolding Energy - sRNA 0.512479 kcal/mol@LB@@LB@Position - mRNA 270 -- 282@LB@Position - sRNA 76 -- 88@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 76 -- 82@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@
32	0.005403	0.5385	b0951	pqiB	-10.24	0.095947	95 -- 108	69 -- 82	paraquat-inducible SoxRS-regulated MCE domain protein	_____________94_____________109\n_____________\|______________\|\n5'-CUG...CAUUA_____U________CGUCA...UUC-3'\n______________AUGUU_GCUUUAGU\n______________\|:\|\|\|_\|\|\|\|\|\|\|\|\n______________UGCAA_CGAAAUCA\n3'-CGC...UCAAG_____C________AUAAG...AAG-5'\n_____________\|______________\|\n_____________83_____________68\n	102 -- 108	69 -- 75	-13.4891 kcal/mol	2.8545 kcal/mol	0.389912 kcal/mol	94 109@LB@ \| \|@LB@5'-CUG...CAUUA U CGUCA...UUC-3'@LB@ AUGUU GCUUUAGU@LB@ \|:\|\|\| \|\|\|\|\|\|\|\|@LB@ UGCAA CGAAAUCA@LB@3'-CGC...UCAAG C AUAAG...AAG-5'@LB@ \| \|@LB@ 83 68@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -13.4891 kcal/mol@LB@Unfolding Energy - mRNA 2.8545 kcal/mol@LB@Unfolding Energy - sRNA 0.389912 kcal/mol@LB@@LB@Position - mRNA 95 -- 108@LB@Position - sRNA 69 -- 82@LB@Position Seed - mRNA 102 -- 108@LB@Position Seed - sRNA 69 -- 75@LB@
147	0.02477	0.5467	b3259	prmA	-10.37	0.091190	111 -- 125	72 -- 88	methyltransferase for 50S ribosomal subunit protein L11	_____________110_______________126\n_____________\|_________________\|\n5'-GCC...CUACU_________________CCUGG...AGG-3'\n______________AAGUUUGC__UGGCUUU\n______________\|\|\|\|\|::\|__\|\|\|\|\|\|\|\n______________UUCAAGUG__ACCGAAA\n3'-CGC...GCGUU________CA_______UCAAU...AAG-5'\n_____________\|_________________\|\n_____________89________________71\n	119 -- 125	72 -- 78	-14.8408 kcal/mol	3.95141 kcal/mol	0.517175 kcal/mol	110 126@LB@ \| \|@LB@5'-GCC...CUACU CCUGG...AGG-3'@LB@ AAGUUUGC UGGCUUU@LB@ \|\|\|\|\|::\| \|\|\|\|\|\|\|@LB@ UUCAAGUG ACCGAAA@LB@3'-CGC...GCGUU CA UCAAU...AAG-5'@LB@ \| \|@LB@ 89 71@LB@@LB@@LB@Energy -10.37 kcal/mol@LB@Hybridization Energy -14.8408 kcal/mol@LB@Unfolding Energy - mRNA 3.95141 kcal/mol@LB@Unfolding Energy - sRNA 0.517175 kcal/mol@LB@@LB@Position - mRNA 111 -- 125@LB@Position - sRNA 72 -- 88@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 72 -- 78@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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