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
149	0.0249	0.5467	b0737	tolQ	-11.44	0.059241	123 -- 143	57 -- 77	membrane spanning protein in TolA-TolQ-TolR complex	_____________122___________________144\n_____________\|_____________________\|\n5'-GCA...GCAGA____C__________C_____CCCAC...CCA-3'\n______________GGUU_UGGUUGUUUG_GUUGA\n______________\|\|:\|_\|:\|\|\|:\|\|:\|_\|\|\|\|\|\n______________CCGA_AUCAAUAAGC_CAACU\n3'-CGC...UGCAA____A__________U_____CUUUG...AAG-5'\n_____________\|_____________________\|\n_____________78____________________56\n	130 -- 136	64 -- 70	-20.7122 kcal/mol	8.05008 kcal/mol	1.21841 kcal/mol	122 144@LB@ \| \|@LB@5'-GCA...GCAGA C C CCCAC...CCA-3'@LB@ GGUU UGGUUGUUUG GUUGA@LB@ \|\|:\| \|:\|\|\|:\|\|:\| \|\|\|\|\|@LB@ CCGA AUCAAUAAGC CAACU@LB@3'-CGC...UGCAA A U CUUUG...AAG-5'@LB@ \| \|@LB@ 78 56@LB@@LB@@LB@Energy -11.44 kcal/mol@LB@Hybridization Energy -20.7122 kcal/mol@LB@Unfolding Energy - mRNA 8.05008 kcal/mol@LB@Unfolding Energy - sRNA 1.21841 kcal/mol@LB@@LB@Position - mRNA 123 -- 143@LB@Position - sRNA 57 -- 77@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 64 -- 70@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@
40	0.008109	0.5385	b0784	moaD	-13.26	0.028244	179 -- 200	15 -- 38	molybdopterin synthase small subunit	_____________178______________________201\n_____________\|________________________\|\n5'-GCA...AGUCG_____________________C__AUGAU...AGC-3'\n______________GGUGACUUUAAGG__UGGAAG_GG\n______________:\|\|\|\|\|\|\|:\|\|\|\|__\|::\|\|\|_\|\|\n______________UCACUGAAGUUCC__AUUUUC_CC\n3'-CGC...GCCCG_____________CA______U__ACGGC...AAG-5'\n_____________\|________________________\|\n_____________39_______________________14\n	185 -- 191	26 -- 32	-24.646 kcal/mol	4.81525 kcal/mol	6.57247 kcal/mol	178 201@LB@ \| \|@LB@5'-GCA...AGUCG C AUGAU...AGC-3'@LB@ GGUGACUUUAAGG UGGAAG GG@LB@ :\|\|\|\|\|\|\|:\|\|\|\| \|::\|\|\| \|\|@LB@ UCACUGAAGUUCC AUUUUC CC@LB@3'-CGC...GCCCG CA U ACGGC...AAG-5'@LB@ \| \|@LB@ 39 14@LB@@LB@@LB@Energy -13.26 kcal/mol@LB@Hybridization Energy -24.646 kcal/mol@LB@Unfolding Energy - mRNA 4.81525 kcal/mol@LB@Unfolding Energy - sRNA 6.57247 kcal/mol@LB@@LB@Position - mRNA 179 -- 200@LB@Position - sRNA 15 -- 38@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 26 -- 32@LB@
179	0.03159	0.5559	b0790	ybhP	-12.03	0.046743	250 -- 264	71 -- 85	endo/exonuclease/phosphatase family protein	_____________249_____________265\n_____________\|_______________\|\n5'-AGU...CAAUA_____AAA_______CCGCG...UUC-3'\n______________UUCAC___GGCUUUA\n______________\|\|\|\|\|___\|\|\|\|\|\|\|\n______________AAGUG___CCGAAAU\n3'-CGC...UUUUC_____CAA_______CAAUA...AAG-5'\n_____________\|_______________\|\n_____________86______________70\n	258 -- 264	71 -- 77	-13.6298 kcal/mol	1.04243 kcal/mol	0.560731 kcal/mol	249 265@LB@ \| \|@LB@5'-AGU...CAAUA AAA CCGCG...UUC-3'@LB@ UUCAC GGCUUUA@LB@ \|\|\|\|\| \|\|\|\|\|\|\|@LB@ AAGUG CCGAAAU@LB@3'-CGC...UUUUC CAA CAAUA...AAG-5'@LB@ \| \|@LB@ 86 70@LB@@LB@@LB@Energy -12.03 kcal/mol@LB@Hybridization Energy -13.6298 kcal/mol@LB@Unfolding Energy - mRNA 1.04243 kcal/mol@LB@Unfolding Energy - sRNA 0.560731 kcal/mol@LB@@LB@Position - mRNA 250 -- 264@LB@Position - sRNA 71 -- 85@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 71 -- 77@LB@
121	0.02058	0.5385	b0796	ybiH	-9.41	0.133616	217 -- 230	24 -- 36	DUF1956 domain-containing tetR family putative transcriptional regulator	_____________216____________231\n_____________\|______________\|\n5'-CGG...UGCCA____AA________GAACA...CCA-3'\n______________UGAC__UCAAGGGU\n______________\|\|\|\|__\|\|\|\|\|\|\|\|\n______________ACUG__AGUUCCCA\n3'-CGC...CCGUC____A_________AUUUU...AAG-5'\n_____________\|______________\|\n_____________37_____________23\n	224 -- 230	24 -- 30	-15.9856 kcal/mol	3.24975 kcal/mol	3.33025 kcal/mol	216 231@LB@ \| \|@LB@5'-CGG...UGCCA AA GAACA...CCA-3'@LB@ UGAC UCAAGGGU@LB@ \|\|\|\| \|\|\|\|\|\|\|\|@LB@ ACUG AGUUCCCA@LB@3'-CGC...CCGUC A AUUUU...AAG-5'@LB@ \| \|@LB@ 37 23@LB@@LB@@LB@Energy -9.41 kcal/mol@LB@Hybridization Energy -15.9856 kcal/mol@LB@Unfolding Energy - mRNA 3.24975 kcal/mol@LB@Unfolding Energy - sRNA 3.33025 kcal/mol@LB@@LB@Position - mRNA 217 -- 230@LB@Position - sRNA 24 -- 36@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 24 -- 30@LB@
184	0.03259	0.5559	b0811	glnH	-9.61	0.123139	215 -- 230	74 -- 90	glutamine transporter subunit	_____________214________________231\n_____________\|__________________\|\n5'-AUC...GUAUU_______U__________GCACU...CCG-3'\n______________AAAAGUU_CAC__UGGCU\n______________\|\|\|\|\|\|\|_\|\|\|__\|\|\|\|\|\n______________UUUUCAA_GUG__ACCGA\n3'-CGC...AGGCG___________CA_____AAUCA...AAG-5'\n_____________\|__________________\|\n_____________91_________________73\n	215 -- 221	84 -- 90	-14.2101 kcal/mol	4.07847 kcal/mol	0.517587 kcal/mol	214 231@LB@ \| \|@LB@5'-AUC...GUAUU U GCACU...CCG-3'@LB@ AAAAGUU CAC UGGCU@LB@ \|\|\|\|\|\|\| \|\|\| \|\|\|\|\|@LB@ UUUUCAA GUG ACCGA@LB@3'-CGC...AGGCG CA AAUCA...AAG-5'@LB@ \| \|@LB@ 91 73@LB@@LB@@LB@Energy -9.61 kcal/mol@LB@Hybridization Energy -14.2101 kcal/mol@LB@Unfolding Energy - mRNA 4.07847 kcal/mol@LB@Unfolding Energy - sRNA 0.517587 kcal/mol@LB@@LB@Position - mRNA 215 -- 230@LB@Position - sRNA 74 -- 90@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 84 -- 90@LB@
21	0.003546	0.5385	b0820	ybiT	-11.98	0.047670	3 -- 23	55 -- 78	ABC-F family putative regulatory ATPase	_____________2________________________24\n_____________\|________________________\|\n_________5'-CC_________GCCA___________AUAUU...UUG-3'\n______________UGGC___AG____UUGGGUUGAGA\n______________\|\|\|\|___\|\|____\|:\|:\|\|\|\|\|\|\|\n______________ACCG___UC____AGCUCAACUCU\n3'-CGC...GUGCA____AAA__AAUA___________UUGAG...AAG-5'\n_____________\|________________________\|\n_____________79_______________________54\n	17 -- 23	55 -- 61	-19.5112 kcal/mol	4.68968 kcal/mol	2.84302 kcal/mol	2 24@LB@ \| \|@LB@ 5'-CC GCCA AUAUU...UUG-3'@LB@ UGGC AG UUGGGUUGAGA@LB@ \|\|\|\| \|\| \|:\|:\|\|\|\|\|\|\|@LB@ ACCG UC AGCUCAACUCU@LB@3'-CGC...GUGCA AAA AAUA UUGAG...AAG-5'@LB@ \| \|@LB@ 79 54@LB@@LB@@LB@Energy -11.98 kcal/mol@LB@Hybridization Energy -19.5112 kcal/mol@LB@Unfolding Energy - mRNA 4.68968 kcal/mol@LB@Unfolding Energy - sRNA 2.84302 kcal/mol@LB@@LB@Position - mRNA 3 -- 23@LB@Position - sRNA 55 -- 78@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 55 -- 61@LB@
6	0.001078	0.5385	b0849	grxA	-11.19	0.065759	209 -- 232	58 -- 81	glutaredoxin 1 redox coenzyme for ribonucleotide reductase (RNR1a)	_____________208______________________233\n_____________\|________________________\|\n5'-AGU...CAAAC____AU_______C__________CCCUU...AUC-3'\n______________CGUU__UUUUGGU_GUUCGGGUUG\n______________\|\|\|\|__:\|\|\|:\|\|_:\|\|\|\|:\|\|\|\|\n______________GCAA__GAAAUCA_UAAGCUCAAC\n3'-CGC...CAAGU____CC_______A__________UCUUU...AAG-5'\n_____________\|________________________\|\n_____________82_______________________57\n	226 -- 232	58 -- 64	-21.2762 kcal/mol	8.79419 kcal/mol	1.29619 kcal/mol	208 233@LB@ \| \|@LB@5'-AGU...CAAAC AU C CCCUU...AUC-3'@LB@ CGUU UUUUGGU GUUCGGGUUG@LB@ \|\|\|\| :\|\|\|:\|\| :\|\|\|\|:\|\|\|\|@LB@ GCAA GAAAUCA UAAGCUCAAC@LB@3'-CGC...CAAGU CC A UCUUU...AAG-5'@LB@ \| \|@LB@ 82 57@LB@@LB@@LB@Energy -11.19 kcal/mol@LB@Hybridization Energy -21.2762 kcal/mol@LB@Unfolding Energy - mRNA 8.79419 kcal/mol@LB@Unfolding Energy - sRNA 1.29619 kcal/mol@LB@@LB@Position - mRNA 209 -- 232@LB@Position - sRNA 58 -- 81@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 58 -- 64@LB@
161	0.02817	0.5559	b0852	rimK	-8.21	0.210781	44 -- 79	81 -- 107	ribosomal protein S6 modification protein	_____________43___________________________________80\n_____________\|____________________________________\|\n5'-AAC...CGCCG____A_______CGAUCAU______C___CAA____UAAAG...AUC-3'\n______________GGAU_CCUGGAG_______AUCCGC_GAA___UCAU\n______________\|\|\|\|_\|\|\|\|\|\|\|_______\|\|\|\|\|\|_:\|\|___\|\|\|:\n______________CCUA_GGACCUC_______UAGGCG_UUU___AGUG\n_________3'-CG_________________________U___CA_____CAACC...AAG-5'\n_____________\|____________________________________\|\n_____________108__________________________________80\n	49 -- 55	97 -- 103	-27.5385 kcal/mol	7.46513 kcal/mol	11.8593 kcal/mol	43 80@LB@ \| \|@LB@5'-AAC...CGCCG A CGAUCAU C CAA UAAAG...AUC-3'@LB@ GGAU CCUGGAG AUCCGC GAA UCAU@LB@ \|\|\|\| \|\|\|\|\|\|\| \|\|\|\|\|\| :\|\| \|\|\|:@LB@ CCUA GGACCUC UAGGCG UUU AGUG@LB@ 3'-CG U CA CAACC...AAG-5'@LB@ \| \|@LB@ 108 80@LB@@LB@@LB@Energy -8.21 kcal/mol@LB@Hybridization Energy -27.5385 kcal/mol@LB@Unfolding Energy - mRNA 7.46513 kcal/mol@LB@Unfolding Energy - sRNA 11.8593 kcal/mol@LB@@LB@Position - mRNA 44 -- 79@LB@Position - sRNA 81 -- 107@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 97 -- 103@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@

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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