Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
67	0.003373	0.1727	b0723	sdhA	-10.29	0.122560	175 -- 204	36 -- 70	succinate dehydrogenase flavoprotein subunit	_____________174_________________________________205\n_____________\|___________________________________\|\n5'-GGU...UUUAU___U____________G______GUG_________AAUUG...GUG-3'\n______________GGA__UC___GUUGUG_UGUGGG____UGUGAUGA\n______________\|\|\|__\|\|___\|:\|\|:\|_:\|\|:::____\|:\|\|\|\|\|\|\n______________CCU__AG___CGACGC_GCAUUU____AUACUACU\n3'-UUU...UGGUC___UU__AAC______G______AAUA________CAAUG...GUG-5'\n_____________\|___________________________________\|\n_____________71__________________________________35\n	198 -- 204	36 -- 42	-24.7755 kcal/mol	5.81881 kcal/mol	8.66537 kcal/mol	174 205@LB@ \| \|@LB@5'-GGU...UUUAU U G GUG AAUUG...GUG-3'@LB@ GGA UC GUUGUG UGUGGG UGUGAUGA@LB@ \|\|\| \|\| \|:\|\|:\| :\|\|::: \|:\|\|\|\|\|\|@LB@ CCU AG CGACGC GCAUUU AUACUACU@LB@3'-UUU...UGGUC UU AAC G AAUA CAAUG...GUG-5'@LB@ \| \|@LB@ 71 35@LB@@LB@@LB@Energy -10.29 kcal/mol@LB@Hybridization Energy -24.7755 kcal/mol@LB@Unfolding Energy - mRNA 5.81881 kcal/mol@LB@Unfolding Energy - sRNA 8.66537 kcal/mol@LB@@LB@Position - mRNA 175 -- 204@LB@Position - sRNA 36 -- 70@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 36 -- 42@LB@
158	0.009324	0.2062	b3574	yiaJ	-10.56	0.109206	175 -- 190	70 -- 85	transcriptional repressor for the yiaKLMNO-lyxK-sgbHUE operon	_____________174______________191\n_____________\|________________\|\n5'-CCC...ACACU________C_______ACGCG...UUG-3'\n______________UUGCGCUA_CAUCAGG\n______________:\|\|\|\|\|:\|_\|\|:\|\|\|\|\n______________GACGCGGU_GUGGUCC\n3'-UUU...CUUAU________U_______CUUUA...GUG-5'\n_____________\|________________\|\n_____________86_______________69\n	184 -- 190	70 -- 76	-22.9924 kcal/mol	5.16069 kcal/mol	7.27689 kcal/mol	174 191@LB@ \| \|@LB@5'-CCC...ACACU C ACGCG...UUG-3'@LB@ UUGCGCUA CAUCAGG@LB@ :\|\|\|\|\|:\| \|\|:\|\|\|\|@LB@ GACGCGGU GUGGUCC@LB@3'-UUU...CUUAU U CUUUA...GUG-5'@LB@ \| \|@LB@ 86 69@LB@@LB@@LB@Energy -10.56 kcal/mol@LB@Hybridization Energy -22.9924 kcal/mol@LB@Unfolding Energy - mRNA 5.16069 kcal/mol@LB@Unfolding Energy - sRNA 7.27689 kcal/mol@LB@@LB@Position - mRNA 175 -- 190@LB@Position - sRNA 70 -- 85@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 70 -- 76@LB@
126	0.006849	0.1914	b2930	yggF	-13.28	0.032133	176 -- 191	68 -- 83	fructose 1 6 bisphosphatase isozyme	_____________175______________192\n_____________\|________________\|\n5'-AUC...AUUUG________________GGCCG...GCC-3'\n______________GCGUUGAUAUCGGGGA\n______________\|\|\|:::\|:\|:\|:\|\|\|\|\n______________CGCGGUUGUGGUCCCU\n3'-UUU...UAUGA________________UUAGA...GUG-5'\n_____________\|________________\|\n_____________84_______________67\n	185 -- 191	68 -- 74	-24.7766 kcal/mol	4.1491 kcal/mol	7.34657 kcal/mol	175 192@LB@ \| \|@LB@5'-AUC...AUUUG GGCCG...GCC-3'@LB@ GCGUUGAUAUCGGGGA@LB@ \|\|\|:::\|:\|:\|:\|\|\|\|@LB@ CGCGGUUGUGGUCCCU@LB@3'-UUU...UAUGA UUAGA...GUG-5'@LB@ \| \|@LB@ 84 67@LB@@LB@@LB@Energy -13.28 kcal/mol@LB@Hybridization Energy -24.7766 kcal/mol@LB@Unfolding Energy - mRNA 4.1491 kcal/mol@LB@Unfolding Energy - sRNA 7.34657 kcal/mol@LB@@LB@Position - mRNA 176 -- 191@LB@Position - sRNA 68 -- 83@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 68 -- 74@LB@
16	0.0007867	0.1666	b2178	yejB	-12.57	0.044336	179 -- 196	66 -- 82	microcin C ABC transporter permease	_____________178________________197\n_____________\|__________________\|\n5'-UGG...CCGUC________AA________GUAGA...GUC-3'\n______________CGCCAGCA__CAGGGAGA\n______________\|\|\|\|\|:\|\|__\|\|\|\|\|\|:\|\n______________GCGGUUGU__GUCCCUUU\n3'-UUU...AUGAC________G_________AGAAC...GUG-5'\n_____________\|__________________\|\n_____________83_________________65\n	190 -- 196	66 -- 72	-25.5869 kcal/mol	5.97553 kcal/mol	7.04029 kcal/mol	178 197@LB@ \| \|@LB@5'-UGG...CCGUC AA GUAGA...GUC-3'@LB@ CGCCAGCA CAGGGAGA@LB@ \|\|\|\|\|:\|\| \|\|\|\|\|\|:\|@LB@ GCGGUUGU GUCCCUUU@LB@3'-UUU...AUGAC G AGAAC...GUG-5'@LB@ \| \|@LB@ 83 65@LB@@LB@@LB@Energy -12.57 kcal/mol@LB@Hybridization Energy -25.5869 kcal/mol@LB@Unfolding Energy - mRNA 5.97553 kcal/mol@LB@Unfolding Energy - sRNA 7.04029 kcal/mol@LB@@LB@Position - mRNA 179 -- 196@LB@Position - sRNA 66 -- 82@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 66 -- 72@LB@
23	0.001421	0.1727	b1234	rssA	-12.55	0.044848	179 -- 192	61 -- 74	putative patatin-like family phospholipase	_____________178____________193\n_____________\|______________\|\n5'-GAU...GCAUU______________CGGGA...AAA-3'\n______________CCAGGGGAAUCUUG\n______________\|\|\|\|\|\|:\|\|\|\|\|\|\|\n______________GGUCCCUUUAGAAC\n3'-UUU...GUUGU______________CGACG...GUG-5'\n_____________\|______________\|\n_____________75_____________60\n	186 -- 192	61 -- 67	-22.3239 kcal/mol	6.14875 kcal/mol	3.62869 kcal/mol	178 193@LB@ \| \|@LB@5'-GAU...GCAUU CGGGA...AAA-3'@LB@ CCAGGGGAAUCUUG@LB@ \|\|\|\|\|\|:\|\|\|\|\|\|\|@LB@ GGUCCCUUUAGAAC@LB@3'-UUU...GUUGU CGACG...GUG-5'@LB@ \| \|@LB@ 75 60@LB@@LB@@LB@Energy -12.55 kcal/mol@LB@Hybridization Energy -22.3239 kcal/mol@LB@Unfolding Energy - mRNA 6.14875 kcal/mol@LB@Unfolding Energy - sRNA 3.62869 kcal/mol@LB@@LB@Position - mRNA 179 -- 192@LB@Position - sRNA 61 -- 74@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 61 -- 67@LB@
91	0.004841	0.1855	b3194	mlaE	-9.16	0.198986	180 -- 189	67 -- 76	ABC transporter maintaining OM lipid asymmetry inner membrane permease protein	_____________179________190\n_____________\|__________\|\n5'-GGA...UCUUU__________UUAAG...GCA-3'\n______________UACCAGGGAG\n______________:\|\|\|\|\|\|\|\|:\n______________GUGGUCCCUU\n3'-UUU...CGGUU__________UAGAA...GUG-5'\n_____________\|__________\|\n_____________77_________66\n	183 -- 189	67 -- 73	-15.9485 kcal/mol	2.86999 kcal/mol	3.9178 kcal/mol	179 190@LB@ \| \|@LB@5'-GGA...UCUUU UUAAG...GCA-3'@LB@ UACCAGGGAG@LB@ :\|\|\|\|\|\|\|\|:@LB@ GUGGUCCCUU@LB@3'-UUU...CGGUU UAGAA...GUG-5'@LB@ \| \|@LB@ 77 66@LB@@LB@@LB@Energy -9.16 kcal/mol@LB@Hybridization Energy -15.9485 kcal/mol@LB@Unfolding Energy - mRNA 2.86999 kcal/mol@LB@Unfolding Energy - sRNA 3.9178 kcal/mol@LB@@LB@Position - mRNA 180 -- 189@LB@Position - sRNA 67 -- 76@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 67 -- 73@LB@
177	0.01048	0.208	b2416	ptsI	-10.21	0.127224	180 -- 212	6 -- 36	PEP-protein phosphotransferase of PTS system (enzyme I)	_____________179________________________________213\n_____________\|__________________________________\|\n5'-GUG...AAAUC___C_____UAA____G___UA__A_________AUUUU...CCG-3'\n______________AGU_ACAAG___GGUA_GGU__UG__UUUCAGGC\n______________\|\|\|_\|\|\|\|\|___\|\|:\|_:\|:__\|\|__\|\|\|\|\|\|\|\|\n______________UCA_UGUUC___CCGU_UCG__AC__AAAGUCCG\n3'-UUU...ACUAC___A____________G___UG__AA________GCGUG-5'\n_____________\|__________________________________\|\n_____________37_________________________________5\n	206 -- 212	6 -- 12	-27.3223 kcal/mol	5.11839 kcal/mol	11.9979 kcal/mol	179 213@LB@ \| \|@LB@5'-GUG...AAAUC C UAA G UA A AUUUU...CCG-3'@LB@ AGU ACAAG GGUA GGU UG UUUCAGGC@LB@ \|\|\| \|\|\|\|\| \|\|:\| :\|: \|\| \|\|\|\|\|\|\|\|@LB@ UCA UGUUC CCGU UCG AC AAAGUCCG@LB@3'-UUU...ACUAC A G UG AA GCGUG-5'@LB@ \| \|@LB@ 37 5@LB@@LB@@LB@Energy -10.21 kcal/mol@LB@Hybridization Energy -27.3223 kcal/mol@LB@Unfolding Energy - mRNA 5.11839 kcal/mol@LB@Unfolding Energy - sRNA 11.9979 kcal/mol@LB@@LB@Position - mRNA 180 -- 212@LB@Position - sRNA 6 -- 36@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 6 -- 12@LB@
195	0.01197	0.2159	b0738	tolR	-7.83	0.338188	180 -- 193	26 -- 40	membrane spanning protein in TolA-TolQ-TolR complex	_____________179_____________194\n_____________\|_______________\|\n5'-UGG...UUAGC______CA_______GUAAG...UGG-3'\n______________GA_GAG__ACAAGGG\n______________\|\|_\|\|\|__\|\|\|\|\|\|\|\n______________CU_CUC__UGUUCCC\n3'-UUU...UAAUA__A___AA_______GUGUC...GUG-5'\n_____________\|_______________\|\n_____________41______________25\n	187 -- 193	26 -- 32	-14.5104 kcal/mol	3.98616 kcal/mol	2.69022 kcal/mol	179 194@LB@ \| \|@LB@5'-UGG...UUAGC CA GUAAG...UGG-3'@LB@ GA GAG ACAAGGG@LB@ \|\| \|\|\| \|\|\|\|\|\|\|@LB@ CU CUC UGUUCCC@LB@3'-UUU...UAAUA A AA GUGUC...GUG-5'@LB@ \| \|@LB@ 41 25@LB@@LB@@LB@Energy -7.83 kcal/mol@LB@Hybridization Energy -14.5104 kcal/mol@LB@Unfolding Energy - mRNA 3.98616 kcal/mol@LB@Unfolding Energy - sRNA 2.69022 kcal/mol@LB@@LB@Position - mRNA 180 -- 193@LB@Position - sRNA 26 -- 40@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 26 -- 32@LB@
62	0.003053	0.1727	b3812	yigB	-11.80	0.062766	182 -- 199	65 -- 83	5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase; pyrimidine phosphatase; riboflavin synthesis	_____________181_________________200\n_____________\|___________________\|\n5'-CUG...UCCAC__________G________AAUGC...GAG-3'\n______________GCGCCAA_AC_GGGGAAAU\n______________\|\|\|\|\|\|\|_\|\|_:\|\|\|\|\|\|\|\n______________CGCGGUU_UG_UCCCUUUA\n3'-UUU...UAUGA_______G__G________GAACC...GUG-5'\n_____________\|___________________\|\n_____________84__________________64\n	193 -- 199	65 -- 71	-28.1563 kcal/mol	8.99645 kcal/mol	7.35968 kcal/mol	181 200@LB@ \| \|@LB@5'-CUG...UCCAC G AAUGC...GAG-3'@LB@ GCGCCAA AC GGGGAAAU@LB@ \|\|\|\|\|\|\| \|\| :\|\|\|\|\|\|\|@LB@ CGCGGUU UG UCCCUUUA@LB@3'-UUU...UAUGA G G GAACC...GUG-5'@LB@ \| \|@LB@ 84 64@LB@@LB@@LB@Energy -11.80 kcal/mol@LB@Hybridization Energy -28.1563 kcal/mol@LB@Unfolding Energy - mRNA 8.99645 kcal/mol@LB@Unfolding Energy - sRNA 7.35968 kcal/mol@LB@@LB@Position - mRNA 182 -- 199@LB@Position - sRNA 65 -- 83@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 65 -- 71@LB@
163	0.009572	0.2068	b4126	yjdI	-8.84	0.226749	182 -- 194	26 -- 41	putative 4Fe-4S mono-cluster protein	_____________181______________195\n_____________\|________________\|\n5'-UAG...CAUAC_______A________AAGGU...GCG-3'\n______________UGAUGAG____GAGGG\n______________\|\|\|\|\|\|\|____:\|\|\|\|\n______________ACUACUC____UUCCC\n3'-UUU...AUAAU_______AAUG_____GUGUC...GUG-5'\n_____________\|________________\|\n_____________42_______________25\n	182 -- 188	35 -- 41	-13.4129 kcal/mol	1.87738 kcal/mol	2.69216 kcal/mol	181 195@LB@ \| \|@LB@5'-UAG...CAUAC A AAGGU...GCG-3'@LB@ UGAUGAG GAGGG@LB@ \|\|\|\|\|\|\| :\|\|\|\|@LB@ ACUACUC UUCCC@LB@3'-UUU...AUAAU AAUG GUGUC...GUG-5'@LB@ \| \|@LB@ 42 25@LB@@LB@@LB@Energy -8.84 kcal/mol@LB@Hybridization Energy -13.4129 kcal/mol@LB@Unfolding Energy - mRNA 1.87738 kcal/mol@LB@Unfolding Energy - sRNA 2.69216 kcal/mol@LB@@LB@Position - mRNA 182 -- 194@LB@Position - sRNA 26 -- 41@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 35 -- 41@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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