Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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	Additional homologs
27	0.0001238	0.01616	b0081	mraZ	-12.77	0.021128	157 -- 196	45 -- 91	RsmH methytransferase inhibitor		_____________156_____________________________________________197\n_____________\|_______________________________________________\|\n5'-GAU...UUUCA___G____________GG_____A____GG___U_____________UGGCA...AAA-3'\n______________GUG_GA___AAUUGUG____GCA__AGU__GAA_AAGG_GGUGAGGC\n______________\|\|:_\|\|___\|\|\|\|\|\|\|____\|\|\|__\|:\|__:\|\|_\|\|\|\|_:\|\|:\|\|:\|\n______________CAU_CU___UUAACAC____CGU__UUA__UUU_UUCC_UCAUUCUG\n3'-UUU...CGCAG___G__UAG_______GAUA___CA___AG___U____U________UUAUA...ACG-5'\n_____________\|_______________________________________________\|\n_____________92______________________________________________44\n	190 -- 196	45 -- 51	-27.6686 kcal/mol	9.1766 kcal/mol	5.72765 kcal/mol	156 197@LB@ \| \|@LB@5'-GAU...UUUCA G GG A GG U UGGCA...AAA-3'@LB@ GUG GA AAUUGUG GCA AGU GAA AAGG GGUGAGGC@LB@ \|\|: \|\| \|\|\|\|\|\|\| \|\|\| \|:\| :\|\| \|\|\|\| :\|\|:\|\|:\|@LB@ CAU CU UUAACAC CGU UUA UUU UUCC UCAUUCUG@LB@3'-UUU...CGCAG G UAG GAUA CA AG U U UUAUA...ACG-5'@LB@ \| \|@LB@ 92 44@LB@@LB@@LB@Energy -12.77 kcal/mol@LB@Hybridization Energy -27.6686 kcal/mol@LB@Unfolding Energy - mRNA 9.1766 kcal/mol@LB@Unfolding Energy - sRNA 5.72765 kcal/mol@LB@@LB@Position - mRNA 157 -- 196@LB@Position - sRNA 45 -- 91@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 45 -- 51@LB@
52	0.0006076	0.04117	b1119	nagK	-11.33	0.051615	175 -- 204	40 -- 71	N-acetyl-D-glucosamine kinase		_____________174_______________________________205\n_____________\|_________________________________\|\n5'-UCA...UAAAG______CA______C______C___________AUUAC...GUG-3'\n______________GCAGUA__UUAAAA_AAGGAG____GGCAAUGU\n______________\|\|\|\|\|\|__\|:\|\|\|\|_\|\|\|\|\|:____\|:\|\|\|\|:\|\n______________CGUCAU__AGUUUU_UUCCUU____CUGUUAUA\n3'-UUU...CGAUA______UA_____________CAUU________CCUCG...ACG-5'\n_____________\|_________________________________\|\n_____________72________________________________39\n	197 -- 203	41 -- 47	-22.8361 kcal/mol	5.88825 kcal/mol	5.61718 kcal/mol	174 205@LB@ \| \|@LB@5'-UCA...UAAAG CA C C AUUAC...GUG-3'@LB@ GCAGUA UUAAAA AAGGAG GGCAAUGU@LB@ \|\|\|\|\|\| \|:\|\|\|\| \|\|\|\|\|: \|:\|\|\|\|:\|@LB@ CGUCAU AGUUUU UUCCUU CUGUUAUA@LB@3'-UUU...CGAUA UA CAUU CCUCG...ACG-5'@LB@ \| \|@LB@ 72 39@LB@@LB@@LB@Energy -11.33 kcal/mol@LB@Hybridization Energy -22.8361 kcal/mol@LB@Unfolding Energy - mRNA 5.88825 kcal/mol@LB@Unfolding Energy - sRNA 5.61718 kcal/mol@LB@@LB@Position - mRNA 175 -- 204@LB@Position - sRNA 40 -- 71@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 41 -- 47@LB@
37	0.0003128	0.02889	b1107	nagZ	-10.24	0.096497	189 -- 204	38 -- 57	beta N-acetyl-glucosaminidase		_____________188__________________205\n_____________\|____________________\|\n5'-AUU...ACAAU____________________GUCCA...CGC-3'\n______________AAGGA___GAG_CAGUGUGG\n______________\|\|\|\|\|___:\|\|_\|\|:\|:\|\|\|\n______________UUCCU___UUC_GUUAUACC\n3'-UUU...GUUUU_____UCA___U________UCGCG...ACG-5'\n_____________\|____________________\|\n_____________58___________________37\n	198 -- 204	38 -- 44	-15.5747 kcal/mol	1.78066 kcal/mol	3.52446 kcal/mol	188 205@LB@ \| \|@LB@5'-AUU...ACAAU GUCCA...CGC-3'@LB@ AAGGA GAG CAGUGUGG@LB@ \|\|\|\|\| :\|\| \|\|:\|:\|\|\|@LB@ UUCCU UUC GUUAUACC@LB@3'-UUU...GUUUU UCA U UCGCG...ACG-5'@LB@ \| \|@LB@ 58 37@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -15.5747 kcal/mol@LB@Unfolding Energy - mRNA 1.78066 kcal/mol@LB@Unfolding Energy - sRNA 3.52446 kcal/mol@LB@@LB@Position - mRNA 189 -- 204@LB@Position - sRNA 38 -- 57@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 38 -- 44@LB@
60	0.001013	0.05816	b2207	napD	-8.99	0.186283	27 -- 46	75 -- 92	assembly protein for periplasmic nitrate reductase		_____________26___________________47\n_____________\|____________________\|\n5'-GUU...CCUGG_____C_________AA___CGCCG...AAG-3'\n______________CGUAU_AGUCAGUUG__UGC\n______________\|\|\|\|:_\|:\|\|\|:\|\|\|__\|\|\|\n______________GCAUG_UUAGUUAAC__ACG\n3'-UUU...CCGCA_____C______________AUACG...ACG-5'\n_____________\|____________________\|\n_____________93___________________74\n	35 -- 41	78 -- 84	-16.0375 kcal/mol	4.6767 kcal/mol	2.37539 kcal/mol	26 47@LB@ \| \|@LB@5'-GUU...CCUGG C AA CGCCG...AAG-3'@LB@ CGUAU AGUCAGUUG UGC@LB@ \|\|\|\|: \|:\|\|\|:\|\|\| \|\|\|@LB@ GCAUG UUAGUUAAC ACG@LB@3'-UUU...CCGCA C AUACG...ACG-5'@LB@ \| \|@LB@ 93 74@LB@@LB@@LB@Energy -8.99 kcal/mol@LB@Hybridization Energy -16.0375 kcal/mol@LB@Unfolding Energy - mRNA 4.6767 kcal/mol@LB@Unfolding Energy - sRNA 2.37539 kcal/mol@LB@@LB@Position - mRNA 27 -- 46@LB@Position - sRNA 75 -- 92@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 78 -- 84@LB@
198	0.008909	0.1548	b2205	napG	-12.90	0.019402	153 -- 203	39 -- 89	ferredoxin-type protein		_____________152_____________________________________________________204\n_____________\|_______________________________________________________\|\n5'-AAG...AAGAG_____CU____GAA____________CAAACU________U______C__U____UCCCG...GGU-3'\n______________ACGGA__UCAA___GUGC___GCGGU______GGAGAAGG__GUAAG_CA_UAUG\n______________\|\|\|:\|__\|\|\|\|___\|\|\|\|___\|\|:\|\|______::\|:\|\|\|\|__\|\|\|\|\|_\|\|_\|\|\|\|\n______________UGCUU__AGUU___CACG___CGUCA______UUUUUUCC__CAUUC_GU_AUAC\n3'-UUU...CAGCA___________AA_____AUA_____UUAAG_________UU_____U__U____CUCGC...ACG-5'\n_____________\|_______________________________________________________\|\n_____________90______________________________________________________38\n	183 -- 189	54 -- 60	-32.365 kcal/mol	12.639 kcal/mol	6.82686 kcal/mol	152 204@LB@ \| \|@LB@5'-AAG...AAGAG CU GAA CAAACU U C U UCCCG...GGU-3'@LB@ ACGGA UCAA GUGC GCGGU GGAGAAGG GUAAG CA UAUG@LB@ \|\|\|:\| \|\|\|\| \|\|\|\| \|\|:\|\| ::\|:\|\|\|\| \|\|\|\|\| \|\| \|\|\|\|@LB@ UGCUU AGUU CACG CGUCA UUUUUUCC CAUUC GU AUAC@LB@3'-UUU...CAGCA AA AUA UUAAG UU U U CUCGC...ACG-5'@LB@ \| \|@LB@ 90 38@LB@@LB@@LB@Energy -12.90 kcal/mol@LB@Hybridization Energy -32.365 kcal/mol@LB@Unfolding Energy - mRNA 12.639 kcal/mol@LB@Unfolding Energy - sRNA 6.82686 kcal/mol@LB@@LB@Position - mRNA 153 -- 203@LB@Position - sRNA 39 -- 89@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 54 -- 60@LB@
5	2.521e-06	0.001776	b3365	nirB	-15.77	0.002536	156 -- 206	35 -- 88	nitrite reductase large subunit NAD(P)H-binding		_____________155____________________________________________________207\n_____________\|______________________________________________________\|\n5'-AUC...GUUGC_______UUAA__G__G_________________A__UC_______AAAU____AAAGU...UUA-3'\n______________UGAAUCG_____G_UA_GCGGUAAU__AGAAAAG_AA__GAGGCAA____GAGC\n______________:\|\|\|\|\|:_____\|_\|\|_\|\|:\|\|\|\|\|__\|:\|\|\|\|\|_\|\|__:\|\|:\|\|\|____\|\|\|\|\n______________GCUUAGU_____C_AU_CGUCAUUA__UUUUUUC_UU__UUCUGUU____CUCG\n3'-UUU...AGCAU_______UAACA_G__A________AG_______C__CA_______AUAC____CGUUG...ACG-5'\n_____________\|______________________________________________________\|\n_____________89_____________________________________________________34\n	192 -- 198	43 -- 49	-31.7984 kcal/mol	7.74851 kcal/mol	8.27555 kcal/mol	155 207@LB@ \| \|@LB@5'-AUC...GUUGC UUAA G G A UC AAAU AAAGU...UUA-3'@LB@ UGAAUCG G UA GCGGUAAU AGAAAAG AA GAGGCAA GAGC@LB@ :\|\|\|\|\|: \| \|\| \|\|:\|\|\|\|\| \|:\|\|\|\|\| \|\| :\|\|:\|\|\| \|\|\|\|@LB@ GCUUAGU C AU CGUCAUUA UUUUUUC UU UUCUGUU CUCG@LB@3'-UUU...AGCAU UAACA G A AG C CA AUAC CGUUG...ACG-5'@LB@ \| \|@LB@ 89 34@LB@@LB@@LB@Energy -15.77 kcal/mol@LB@Hybridization Energy -31.7984 kcal/mol@LB@Unfolding Energy - mRNA 7.74851 kcal/mol@LB@Unfolding Energy - sRNA 8.27555 kcal/mol@LB@@LB@Position - mRNA 156 -- 206@LB@Position - sRNA 35 -- 88@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 43 -- 49@LB@
195	0.008697	0.1548	b0192	nlpE	-11.98	0.034903	167 -- 206	41 -- 78	lipoprotein involved with copper homeostasis and adhesion		_____________166________________________________________207\n_____________\|__________________________________________\|\n5'-UCA...GCAAA____GCA_____CGGG___AA__________U__________AAAAA...CGC-3'\n______________GUGC___GCGGU____AAU__AAAGAAGGAA___GGAUGGUG\n______________\|\|\|\|___\|\|:\|\|____\|\|\|__\|\|\|:\|\|\|\|\|\|___:\|\|:::\|:\n______________CACG___CGUCA____UUA__UUUUUUCCUU___UCUGUUAU\n3'-UUU...GUUAA____AUA____________AG__________CAU________ACCUC...ACG-5'\n_____________\|__________________________________________\|\n_____________79_________________________________________40\n	200 -- 206	41 -- 47	-26.7874 kcal/mol	9.04038 kcal/mol	5.77415 kcal/mol	166 207@LB@ \| \|@LB@5'-UCA...GCAAA GCA CGGG AA U AAAAA...CGC-3'@LB@ GUGC GCGGU AAU AAAGAAGGAA GGAUGGUG@LB@ \|\|\|\| \|\|:\|\| \|\|\| \|\|\|:\|\|\|\|\|\| :\|\|:::\|:@LB@ CACG CGUCA UUA UUUUUUCCUU UCUGUUAU@LB@3'-UUU...GUUAA AUA AG CAU ACCUC...ACG-5'@LB@ \| \|@LB@ 79 40@LB@@LB@@LB@Energy -11.98 kcal/mol@LB@Hybridization Energy -26.7874 kcal/mol@LB@Unfolding Energy - mRNA 9.04038 kcal/mol@LB@Unfolding Energy - sRNA 5.77415 kcal/mol@LB@@LB@Position - mRNA 167 -- 206@LB@Position - sRNA 41 -- 78@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 41 -- 47@LB@
185	0.008022	0.1528	b1813	nudL	-20.51	0.000035	188 -- 228	15 -- 56	putative CoA pyrophosphohydrolase weak 3-phosphohydroxypyruvate phosphatase		_____________187____________________________________________229\n_____________\|______________________________________________\|\n5'-CCU...CAACU__A__________________AUAC_________G___________AUUUU...CUG-3'\n______________GG_GAAGUAAGAC___GUGGA____CGUAGC_CU_A_CGCUUGAUG\n______________:\|_\|\|\|\|\|\|\|\|\|\|___:\|\|\|\|____\|\|:\|:\|_\|:_\|_\|\|\|\|\|\|\|:\|\n______________UC_CUUCAUUCUG___UACCU____GCGUUG_GG_U_GCGAACUGC\n3'-UUU...UUUUU_____________UUA_____C_________C__G_A_________AACGU...ACG-5'\n_____________\|______________________________________________\|\n_____________57_____________________________________________14\n	221 -- 227	16 -- 22	-41.758 kcal/mol	7.45502 kcal/mol	13.7937 kcal/mol	187 229@LB@ \| \|@LB@5'-CCU...CAACU A AUAC G AUUUU...CUG-3'@LB@ GG GAAGUAAGAC GUGGA CGUAGC CU A CGCUUGAUG@LB@ :\| \|\|\|\|\|\|\|\|\|\| :\|\|\|\| \|\|:\|:\| \|: \| \|\|\|\|\|\|\|:\|@LB@ UC CUUCAUUCUG UACCU GCGUUG GG U GCGAACUGC@LB@3'-UUU...UUUUU UUA C C G A AACGU...ACG-5'@LB@ \| \|@LB@ 57 14@LB@@LB@@LB@Energy -20.51 kcal/mol@LB@Hybridization Energy -41.758 kcal/mol@LB@Unfolding Energy - mRNA 7.45502 kcal/mol@LB@Unfolding Energy - sRNA 13.7937 kcal/mol@LB@@LB@Position - mRNA 188 -- 228@LB@Position - sRNA 15 -- 56@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 16 -- 22@LB@
46	0.0004731	0.03623	b2279	nuoK	-14.07	0.008802	136 -- 157	69 -- 92	NADH:ubiquinone oxidoreductase membrane subunit K		_____________135______________________158\n_____________\|________________________\|\n5'-GGU...AAGAG_________G__________A___AUCGU...UUG-3'\n______________CGUGCGGGU_AA__GUGCUG_GCA\n______________\|\|\|:\|\|::\|_\|\|__\|\|\|\|\|:_\|\|\|\n______________GCAUGCUUA_UU__CACGAU_CGU\n3'-UUU...CCGCA_________G__AA______A___CAUUA...ACG-5'\n_____________\|________________________\|\n_____________93_______________________68\n	138 -- 144	84 -- 90	-25.4547 kcal/mol	6.72556 kcal/mol	4.66371 kcal/mol	135 158@LB@ \| \|@LB@5'-GGU...AAGAG G A AUCGU...UUG-3'@LB@ CGUGCGGGU AA GUGCUG GCA@LB@ \|\|\|:\|\|::\| \|\| \|\|\|\|\|: \|\|\|@LB@ GCAUGCUUA UU CACGAU CGU@LB@3'-UUU...CCGCA G AA A CAUUA...ACG-5'@LB@ \| \|@LB@ 93 68@LB@@LB@@LB@Energy -14.07 kcal/mol@LB@Hybridization Energy -25.4547 kcal/mol@LB@Unfolding Energy - mRNA 6.72556 kcal/mol@LB@Unfolding Energy - sRNA 4.66371 kcal/mol@LB@@LB@Position - mRNA 136 -- 157@LB@Position - sRNA 69 -- 92@LB@Position Seed - mRNA 138 -- 144@LB@Position Seed - sRNA 84 -- 90@LB@
50	0.0005726	0.04013	b2215	ompC	-10.22	0.097386	138 -- 180	44 -- 87	outer membrane porin protein C	b0929 b0241 b1377	_____________137___________________________________________181\n_____________\|_____________________________________________\|\n5'-AUC...AAUGA________CAG____________CA________CAAAUA______UAUAA...AUC-3'\n______________GGGUUAAU_____UAUGCAGUGG__UAAAAAAG______AAGGCA\n______________\|::\|:\|\|\|_____\|\|\|\|\|\|\|\|::__:\|\|\|\|\|\|\|______\|\|\|:\|\|\n______________CUUAGUUA_____AUACGUCAUU__GUUUUUUC______UUCUGU\n3'-UUU...GCAUG________ACACG__________AA________CUUCA_______UAUAC...ACG-5'\n_____________\|_____________________________________________\|\n_____________88____________________________________________43\n	162 -- 168	55 -- 61	-25.937 kcal/mol	10.0096 kcal/mol	5.70573 kcal/mol	137 181@LB@ \| \|@LB@5'-AUC...AAUGA CAG CA CAAAUA UAUAA...AUC-3'@LB@ GGGUUAAU UAUGCAGUGG UAAAAAAG AAGGCA@LB@ \|::\|:\|\|\| \|\|\|\|\|\|\|\|:: :\|\|\|\|\|\|\| \|\|\|:\|\|@LB@ CUUAGUUA AUACGUCAUU GUUUUUUC UUCUGU@LB@3'-UUU...GCAUG ACACG AA CUUCA UAUAC...ACG-5'@LB@ \| \|@LB@ 88 43@LB@@LB@@LB@Energy -10.22 kcal/mol@LB@Hybridization Energy -25.937 kcal/mol@LB@Unfolding Energy - mRNA 10.0096 kcal/mol@LB@Unfolding Energy - sRNA 5.70573 kcal/mol@LB@@LB@Position - mRNA 138 -- 180@LB@Position - sRNA 44 -- 87@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 55 -- 61@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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