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
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@
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@
23	0.004272	0.5385	b3315	rplV	-10.64	0.081808	245 -- 278	60 -- 90	50S ribosomal subunit protein L22	_____________244________________________________279\n_____________\|__________________________________\|\n5'-CGC...GCUCA__________C___UU___GACCUG_____C___AAGAA...UGG-3'\n______________GAAGGUUCGC_UUG__GCU______AUUCG_GGU\n______________:\|\|:\|\|\|\|:\|_\|\|\|__\|\|\|______\|\|\|\|\|_:\|\|\n______________UUUUCAAGUG_AAC__CGA______UAAGC_UCA\n3'-CGC...AGGCG__________C________AAUCAA_________ACUCU...AAG-5'\n_____________\|__________________________________\|\n_____________91_________________________________59\n	248 -- 254	81 -- 87	-21.0379 kcal/mol	8.68511 kcal/mol	1.70935 kcal/mol	244 279@LB@ \| \|@LB@5'-CGC...GCUCA C UU GACCUG C AAGAA...UGG-3'@LB@ GAAGGUUCGC UUG GCU AUUCG GGU@LB@ :\|\|:\|\|\|\|:\| \|\|\| \|\|\| \|\|\|\|\| :\|\|@LB@ UUUUCAAGUG AAC CGA UAAGC UCA@LB@3'-CGC...AGGCG C AAUCAA ACUCU...AAG-5'@LB@ \| \|@LB@ 91 59@LB@@LB@@LB@Energy -10.64 kcal/mol@LB@Hybridization Energy -21.0379 kcal/mol@LB@Unfolding Energy - mRNA 8.68511 kcal/mol@LB@Unfolding Energy - sRNA 1.70935 kcal/mol@LB@@LB@Position - mRNA 245 -- 278@LB@Position - sRNA 60 -- 90@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 81 -- 87@LB@
24	0.00428	0.5385	b0090	murG	-10.85	0.075280	191 -- 203	77 -- 89	N-acetylglucosaminyl transferase	_____________190___________204\n_____________\|_____________\|\n5'-AUU...UGUAC__________A__AGUGG...GUU-3'\n______________GAGGUUCACG_UG\n______________:\|:\|\|\|\|\|\|\|_\|\|\n______________UUUCAAGUGC_AC\n3'-CGC...GGCGU__________A__CGAAA...AAG-5'\n_____________\|_____________\|\n_____________90____________76\n	194 -- 200	80 -- 86	-14.5499 kcal/mol	3.18923 kcal/mol	0.510111 kcal/mol	190 204@LB@ \| \|@LB@5'-AUU...UGUAC A AGUGG...GUU-3'@LB@ GAGGUUCACG UG@LB@ :\|:\|\|\|\|\|\|\| \|\|@LB@ UUUCAAGUGC AC@LB@3'-CGC...GGCGU A CGAAA...AAG-5'@LB@ \| \|@LB@ 90 76@LB@@LB@@LB@Energy -10.85 kcal/mol@LB@Hybridization Energy -14.5499 kcal/mol@LB@Unfolding Energy - mRNA 3.18923 kcal/mol@LB@Unfolding Energy - sRNA 0.510111 kcal/mol@LB@@LB@Position - mRNA 191 -- 203@LB@Position - sRNA 77 -- 89@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 80 -- 86@LB@
25	0.004715	0.5385	b0009	mog	-11.66	0.054310	209 -- 227	68 -- 85	molybdochelatase incorporating molybdenum into molybdopterin	_____________208__________________228\n_____________\|____________________\|\n5'-UGG...AAUAC_______AU___________UCCAU...CAU-3'\n______________UUUACGU__UGGC_UUAGUU\n______________\|\|:\|\|\|\|__\|\|\|\|_\|\|\|\|\|\|\n______________AAGUGCA__ACCG_AAUCAA\n3'-CGC...UUUUC_____________A______UAAGC...AAG-5'\n_____________\|____________________\|\n_____________86___________________67\n	209 -- 215	79 -- 85	-16.6663 kcal/mol	4.44065 kcal/mol	0.567776 kcal/mol	208 228@LB@ \| \|@LB@5'-UGG...AAUAC AU UCCAU...CAU-3'@LB@ UUUACGU UGGC UUAGUU@LB@ \|\|:\|\|\|\| \|\|\|\| \|\|\|\|\|\|@LB@ AAGUGCA ACCG AAUCAA@LB@3'-CGC...UUUUC A UAAGC...AAG-5'@LB@ \| \|@LB@ 86 67@LB@@LB@@LB@Energy -11.66 kcal/mol@LB@Hybridization Energy -16.6663 kcal/mol@LB@Unfolding Energy - mRNA 4.44065 kcal/mol@LB@Unfolding Energy - sRNA 0.567776 kcal/mol@LB@@LB@Position - mRNA 209 -- 227@LB@Position - sRNA 68 -- 85@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 79 -- 85@LB@
26	0.00484	0.5385	b3033	yqiB	-11.20	0.065436	106 -- 117	15 -- 27	DUF1249 protein YqiB	_____________105___________118\n_____________\|_____________\|\n5'-UGG...CCAGU_____________GGAAA...GCG-3'\n______________GGG_UAGAAGAGG\n______________\|\|\|_\|\|:\|\|\|\|\|\|\n______________CCC_AUUUUCUCC\n3'-CGC...AAGUU___A_________ACGGC...AAG-5'\n_____________\|_____________\|\n_____________28____________14\n	111 -- 117	15 -- 21	-17.3581 kcal/mol	2.92425 kcal/mol	3.23583 kcal/mol	105 118@LB@ \| \|@LB@5'-UGG...CCAGU GGAAA...GCG-3'@LB@ GGG UAGAAGAGG@LB@ \|\|\| \|\|:\|\|\|\|\|\|@LB@ CCC AUUUUCUCC@LB@3'-CGC...AAGUU A ACGGC...AAG-5'@LB@ \| \|@LB@ 28 14@LB@@LB@@LB@Energy -11.20 kcal/mol@LB@Hybridization Energy -17.3581 kcal/mol@LB@Unfolding Energy - mRNA 2.92425 kcal/mol@LB@Unfolding Energy - sRNA 3.23583 kcal/mol@LB@@LB@Position - mRNA 106 -- 117@LB@Position - sRNA 15 -- 27@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 15 -- 21@LB@
27	0.005053	0.5385	b2058	wcaB	-11.44	0.059229	168 -- 190	61 -- 82	putative acyl transferase	_____________167______________________191\n_____________\|________________________\|\n5'-ACC...GGCAA____C_____GA____________GGCGC...AGA-3'\n______________ACGU_UGGCU__UGG_UAUUCGGG\n______________\|\|\|\|_\|\|\|\|\|__\|:\|_\|\|\|\|\|\|:\|\n______________UGCA_ACCGA__AUC_AUAAGCUC\n3'-CGC...UCAAG__________A____A________AACUC...AAG-5'\n_____________\|________________________\|\n_____________83_______________________60\n	184 -- 190	61 -- 67	-21.3941 kcal/mol	8.91056 kcal/mol	1.03929 kcal/mol	167 191@LB@ \| \|@LB@5'-ACC...GGCAA C GA GGCGC...AGA-3'@LB@ ACGU UGGCU UGG UAUUCGGG@LB@ \|\|\|\| \|\|\|\|\| \|:\| \|\|\|\|\|\|:\|@LB@ UGCA ACCGA AUC AUAAGCUC@LB@3'-CGC...UCAAG A A AACUC...AAG-5'@LB@ \| \|@LB@ 83 60@LB@@LB@@LB@Energy -11.44 kcal/mol@LB@Hybridization Energy -21.3941 kcal/mol@LB@Unfolding Energy - mRNA 8.91056 kcal/mol@LB@Unfolding Energy - sRNA 1.03929 kcal/mol@LB@@LB@Position - mRNA 168 -- 190@LB@Position - sRNA 61 -- 82@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 61 -- 67@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@
29	0.005218	0.5385	b3433	asd	-11.22	0.064904	208 -- 219	71 -- 82	aspartate-semialdehyde dehydrogenase NAD(P)-binding	_____________207__________220\n_____________\|____________\|\n5'-UCA...GAAAA____________UCGGC...UCU-3'\n______________AUGUUGGUUUUA\n______________\|:\|\|\|\|\|:\|\|\|\|\n______________UGCAACCGAAAU\n3'-CGC...UCAAG____________CAAUA...AAG-5'\n_____________\|____________\|\n_____________83___________70\n	213 -- 219	71 -- 77	-13.9075 kcal/mol	2.30708 kcal/mol	0.38228 kcal/mol	207 220@LB@ \| \|@LB@5'-UCA...GAAAA UCGGC...UCU-3'@LB@ AUGUUGGUUUUA@LB@ \|:\|\|\|\|\|:\|\|\|\|@LB@ UGCAACCGAAAU@LB@3'-CGC...UCAAG CAAUA...AAG-5'@LB@ \| \|@LB@ 83 70@LB@@LB@@LB@Energy -11.22 kcal/mol@LB@Hybridization Energy -13.9075 kcal/mol@LB@Unfolding Energy - mRNA 2.30708 kcal/mol@LB@Unfolding Energy - sRNA 0.38228 kcal/mol@LB@@LB@Position - mRNA 208 -- 219@LB@Position - sRNA 71 -- 82@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 71 -- 77@LB@
30	0.005373	0.5385	b1624	ydgJ	-10.76	0.078067	229 -- 247	61 -- 79	putative oxidoreductase	_____________228_________________248\n_____________\|___________________\|\n5'-GUA...GUUGA____G_A_______G____CAAAA...CGG-3'\n______________UUGG_U_UGGUUAU_CGAG\n______________\|\|\|\|_\|_\|:\|\|\|\|\|_\|\|\|\|\n______________AACC_A_AUCAAUA_GCUC\n3'-CGC...AGUGC____G_A_______A____AACUC...AAG-5'\n_____________\|___________________\|\n_____________80__________________60\n	236 -- 242	66 -- 72	-16.8363 kcal/mol	5.27817 kcal/mol	0.798019 kcal/mol	228 248@LB@ \| \|@LB@5'-GUA...GUUGA G A G CAAAA...CGG-3'@LB@ UUGG U UGGUUAU CGAG@LB@ \|\|\|\| \| \|:\|\|\|\|\| \|\|\|\|@LB@ AACC A AUCAAUA GCUC@LB@3'-CGC...AGUGC G A A AACUC...AAG-5'@LB@ \| \|@LB@ 80 60@LB@@LB@@LB@Energy -10.76 kcal/mol@LB@Hybridization Energy -16.8363 kcal/mol@LB@Unfolding Energy - mRNA 5.27817 kcal/mol@LB@Unfolding Energy - sRNA 0.798019 kcal/mol@LB@@LB@Position - mRNA 229 -- 247@LB@Position - sRNA 61 -- 79@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 66 -- 72@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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