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
121	0.004137	0.1205	b0353	mhpT	-11.58	0.044392	170 -- 179	1 -- 10	3-hydroxyphenylpropionic transporter		_____________169________180\n_____________\|__________\|\n5'-CGG...UCGCG__________ACUCG...CGG-3'\n______________AUUCACCUGC\n______________\|\|\|\|\|\|\|\|\|\|\n______________UAAGUGGACG\n3'-UUU...CAACG__________-5'\n_____________\|_________\|\n_____________11________1\n	173 -- 179	1 -- 7	-16.6324 kcal/mol	2.26547 kcal/mol	2.7891 kcal/mol	169 180@LB@ \| \|@LB@5'-CGG...UCGCG ACUCG...CGG-3'@LB@ AUUCACCUGC@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UAAGUGGACG@LB@3'-UUU...CAACG -5'@LB@ \| \|@LB@ 11 1@LB@@LB@@LB@Energy -11.58 kcal/mol@LB@Hybridization Energy -16.6324 kcal/mol@LB@Unfolding Energy - mRNA 2.26547 kcal/mol@LB@Unfolding Energy - sRNA 2.7891 kcal/mol@LB@@LB@Position - mRNA 170 -- 179@LB@Position - sRNA 1 -- 10@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 1 -- 7@LB@
122	0.004264	0.1231	b2914	rpiA	-10.11	0.103884	190 -- 234	45 -- 89	ribose 5-phosphate isomerase constitutive		_____________189______________________________________________235\n_____________\|________________________________________________\|\n5'-GAA...CACAG_____A____CA__AC______GAUGA___G_______C_________GGGCG...CAC-3'\n______________GCGAA_CGAU__UG____GCAG_____AUU_AAAAAAG__AGUAGGAU\n______________:\|\|\|\|_\|:\|\|__\|\|____\|\|\|\|_____\|\|\|_\|\|\|\|\|\|\|__\|\|\|\|:\|\|:\n______________UGCUU_GUUA__AC____CGUC_____UAA_UUUUUUC__UCAUUCUG\n3'-UUU...CAGCA_____A____AC__GAUA____AU______G_______CU________UUAUA...ACG-5'\n_____________\|________________________________________________\|\n_____________90_______________________________________________44\n	228 -- 234	45 -- 51	-27.3521 kcal/mol	11.527 kcal/mol	5.72096 kcal/mol	189 235@LB@ \| \|@LB@5'-GAA...CACAG A CA AC GAUGA G C GGGCG...CAC-3'@LB@ GCGAA CGAU UG GCAG AUU AAAAAAG AGUAGGAU@LB@ :\|\|\|\| \|:\|\| \|\| \|\|\|\| \|\|\| \|\|\|\|\|\|\| \|\|\|\|:\|\|:@LB@ UGCUU GUUA AC CGUC UAA UUUUUUC UCAUUCUG@LB@3'-UUU...CAGCA A AC GAUA AU G CU UUAUA...ACG-5'@LB@ \| \|@LB@ 90 44@LB@@LB@@LB@Energy -10.11 kcal/mol@LB@Hybridization Energy -27.3521 kcal/mol@LB@Unfolding Energy - mRNA 11.527 kcal/mol@LB@Unfolding Energy - sRNA 5.72096 kcal/mol@LB@@LB@Position - mRNA 190 -- 234@LB@Position - sRNA 45 -- 89@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 45 -- 51@LB@
123	0.004425	0.1258	b2535	csiE	-7.63	0.347411	1 -- 40	5 -- 36	stationary phase inducible protein		______________1_______________________________________41\n______________\|_______________________________________\|\n___________5'-__AG___UAA____UGA_____A_C___AUAAU_______AAAAC...UGG-3'\n______________GC__AAC___CCCA___UCGCU_G_ACG_____CAUUCAC\n______________\|\|__\|\|\|___\|\|\|\|___\|\|\|\|\|_\|_\|\|\|_____\|\|\|\|\|\|\|\n______________CG__UUG___GGGU___AGCGA_C_UGC_____GUAAGUG\n3'-UUU...UACCU__CG___C______________A_____AAC_________GACG-5'\n_____________\|________________________________________\|\n_____________37_______________________________________4\n	34 -- 40	5 -- 11	-25.9316 kcal/mol	3.04784 kcal/mol	15.2569 kcal/mol	1 41@LB@ \| \|@LB@ 5'- AG UAA UGA A C AUAAU AAAAC...UGG-3'@LB@ GC AAC CCCA UCGCU G ACG CAUUCAC@LB@ \|\| \|\|\| \|\|\|\| \|\|\|\|\| \| \|\|\| \|\|\|\|\|\|\|@LB@ CG UUG GGGU AGCGA C UGC GUAAGUG@LB@3'-UUU...UACCU CG C A AAC GACG-5'@LB@ \| \|@LB@ 37 4@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -25.9316 kcal/mol@LB@Unfolding Energy - mRNA 3.04784 kcal/mol@LB@Unfolding Energy - sRNA 15.2569 kcal/mol@LB@@LB@Position - mRNA 1 -- 40@LB@Position - sRNA 5 -- 36@LB@Position Seed - mRNA 34 -- 40@LB@Position Seed - sRNA 5 -- 11@LB@
124	0.004441	0.1258	b1656	sodB	-12.34	0.027802	164 -- 220	1 -- 93	superoxide dismutase Fe		_____________163____________________________________________________________________________________________221\n_____________\|______________________________________________________________________________________________\|\n5'-UCU...GGCUA_________________________AAUUAA___U________________________A________AU___AA___________________ACUAC...AGA-3'\n______________UUGUACG____________UAUGCA______UAA_AAAGGA______________GAGU_GCAAUGUC__UCG_____________UUACCUGC\n______________\|:\|\|\|\|\|____________\|\|\|\|\|\|______:\|\|_\|\|\|\|\|\|______________\|\|\|:_\|\|\|\|:\|:\|__\|\|\|_____________\|:\|\|\|\|\|\|\n______________AGCAUGC____________AUACGU______GUU_UUUCCU______________CUCG_CGUUGCGG__AGC_____________AGUGGACG\n3'-UUU...GCCGC_______UUAGUUAACACG______CAUUAA___U______UCAUUCUGUUAUAC_____________GU___GAACUGCAACGUA________-5'\n_____________\|_____________________________________________________________________________________________\|\n_____________94____________________________________________________________________________________________1\n	214 -- 220	1 -- 7	-45.1977 kcal/mol	11.9384 kcal/mol	20.925 kcal/mol	163 221@LB@ \| \|@LB@5'-UCU...GGCUA AAUUAA U A AU AA ACUAC...AGA-3'@LB@ UUGUACG UAUGCA UAA AAAGGA GAGU GCAAUGUC UCG UUACCUGC@LB@ \|:\|\|\|\|\| \|\|\|\|\|\| :\|\| \|\|\|\|\|\| \|\|\|: \|\|\|\|:\|:\| \|\|\| \|:\|\|\|\|\|\|@LB@ AGCAUGC AUACGU GUU UUUCCU CUCG CGUUGCGG AGC AGUGGACG@LB@3'-UUU...GCCGC UUAGUUAACACG CAUUAA U UCAUUCUGUUAUAC GU GAACUGCAACGUA -5'@LB@ \| \|@LB@ 94 1@LB@@LB@@LB@Energy -12.34 kcal/mol@LB@Hybridization Energy -45.1977 kcal/mol@LB@Unfolding Energy - mRNA 11.9384 kcal/mol@LB@Unfolding Energy - sRNA 20.925 kcal/mol@LB@@LB@Position - mRNA 164 -- 220@LB@Position - sRNA 1 -- 93@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 1 -- 7@LB@
125	0.004538	0.1258	b0951	pqiB	-12.90	0.019327	185 -- 205	37 -- 57	paraquat-inducible SoxRS-regulated MCE domain protein		_____________184___________________206\n_____________\|_____________________\|\n5'-CUG...AGCAU______UCCU___________AUCUA...UUC-3'\n______________GAGGAG____GACAGUAUGGA\n______________:\|\|\|\|:____\|\|\|\|:\|\|\|\|\|\|\n______________UUCCUU____CUGUUAUACCU\n3'-UUU...GUUUU______CAUU___________CGCGU...ACG-5'\n_____________\|_____________________\|\n_____________58____________________36\n	199 -- 205	37 -- 43	-21.8788 kcal/mol	5.24969 kcal/mol	3.68958 kcal/mol	184 206@LB@ \| \|@LB@5'-CUG...AGCAU UCCU AUCUA...UUC-3'@LB@ GAGGAG GACAGUAUGGA@LB@ :\|\|\|\|: \|\|\|\|:\|\|\|\|\|\|@LB@ UUCCUU CUGUUAUACCU@LB@3'-UUU...GUUUU CAUU CGCGU...ACG-5'@LB@ \| \|@LB@ 58 36@LB@@LB@@LB@Energy -12.90 kcal/mol@LB@Hybridization Energy -21.8788 kcal/mol@LB@Unfolding Energy - mRNA 5.24969 kcal/mol@LB@Unfolding Energy - sRNA 3.68958 kcal/mol@LB@@LB@Position - mRNA 185 -- 205@LB@Position - sRNA 37 -- 57@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 37 -- 43@LB@
126	0.004539	0.1258	b0546	ybcM	-11.00	0.062763	188 -- 220	45 -- 91	DLP12 prophage; putative DNA-binding transcriptional regulator	b1499 b0564 b3515 b4116 b0566 b3516	_____________187_____________________________________________221\n_____________\|_______________________________________________\|\n5'-GCU...AUAAA___G__UGA__GUA_________A_______________________UAACU...GUC-3'\n______________GUA_GG___GA___UGCUG_GCA______________GAGGUAAGAC\n______________\|\|\|_\|:___:\|___\|\|\|\|:_\|\|\|______________\|\|:\|\|\|\|\|\|\|\n______________CAU_CU___UU___ACGAU_CGU______________CUUCAUUCUG\n3'-UUU...CGCAG___G__UAG__AAC_____A___CAUUAAGUUUUUUC__________UUAUA...ACG-5'\n_____________\|_______________________________________________\|\n_____________92______________________________________________44\n	214 -- 220	45 -- 51	-23.4531 kcal/mol	6.72952 kcal/mol	5.72765 kcal/mol	187 221@LB@ \| \|@LB@5'-GCU...AUAAA G UGA GUA A UAACU...GUC-3'@LB@ GUA GG GA UGCUG GCA GAGGUAAGAC@LB@ \|\|\| \|: :\| \|\|\|\|: \|\|\| \|\|:\|\|\|\|\|\|\|@LB@ CAU CU UU ACGAU CGU CUUCAUUCUG@LB@3'-UUU...CGCAG G UAG AAC A CAUUAAGUUUUUUC UUAUA...ACG-5'@LB@ \| \|@LB@ 92 44@LB@@LB@@LB@Energy -11.00 kcal/mol@LB@Hybridization Energy -23.4531 kcal/mol@LB@Unfolding Energy - mRNA 6.72952 kcal/mol@LB@Unfolding Energy - sRNA 5.72765 kcal/mol@LB@@LB@Position - mRNA 188 -- 220@LB@Position - sRNA 45 -- 91@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 45 -- 51@LB@
127	0.004567	0.1258	b2320	pdxB	-8.62	0.223386	291 -- 299	20 -- 28	erythronate-4-phosphate dehydrogenase		_____________290_______300\n_____________\|_________\|\n5'-ACG...CAAUC_________C-3'\n______________CCCGUCGCU\n______________\|\|\|:\|\|\|\|\|\n______________GGGUAGCGA\n3'-UUU...GUUGC_________ACUGC...ACG-5'\n_____________\|_________\|\n_____________29________19\n	293 -- 299	20 -- 26	-15.7186 kcal/mol	1.54056 kcal/mol	5.56153 kcal/mol	290 300@LB@ \| \|@LB@5'-ACG...CAAUC C-3'@LB@ CCCGUCGCU@LB@ \|\|\|:\|\|\|\|\|@LB@ GGGUAGCGA@LB@3'-UUU...GUUGC ACUGC...ACG-5'@LB@ \| \|@LB@ 29 19@LB@@LB@@LB@Energy -8.62 kcal/mol@LB@Hybridization Energy -15.7186 kcal/mol@LB@Unfolding Energy - mRNA 1.54056 kcal/mol@LB@Unfolding Energy - sRNA 5.56153 kcal/mol@LB@@LB@Position - mRNA 291 -- 299@LB@Position - sRNA 20 -- 28@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 20 -- 26@LB@
128	0.004569	0.1258	b3033	yqiB	-9.35	0.155553	90 -- 130	43 -- 87	DUF1249 protein YqiB		_____________89_____________________________________________131\n_____________\|______________________________________________\|\n5'-UGG...GCCGG_____________AUAC______GUA__________AAAUC_____CGCAG...GCG-3'\n______________GAA_CAG____GC____CAGUGG___GAAGAGGGGA_____GACAA\n______________\|\|\|_\|\|:____\|\|____\|\|\|\|::___:\|\|:\|:\|\|:\|_____\|\|\|\|\|\n______________CUU_GUU____CG____GUCAUU___UUUUUUCCUU_____CUGUU\n3'-UUU...GCAUG___A___AACA__AUAC______AAG__________CAUU______AUACC...ACG-5'\n_____________\|______________________________________________\|\n_____________88_____________________________________________42\n	114 -- 120	52 -- 58	-22.1335 kcal/mol	7.07839 kcal/mol	5.71172 kcal/mol	89 131@LB@ \| \|@LB@5'-UGG...GCCGG AUAC GUA AAAUC CGCAG...GCG-3'@LB@ GAA CAG GC CAGUGG GAAGAGGGGA GACAA@LB@ \|\|\| \|\|: \|\| \|\|\|\|:: :\|\|:\|:\|\|:\| \|\|\|\|\|@LB@ CUU GUU CG GUCAUU UUUUUUCCUU CUGUU@LB@3'-UUU...GCAUG A AACA AUAC AAG CAUU AUACC...ACG-5'@LB@ \| \|@LB@ 88 42@LB@@LB@@LB@Energy -9.35 kcal/mol@LB@Hybridization Energy -22.1335 kcal/mol@LB@Unfolding Energy - mRNA 7.07839 kcal/mol@LB@Unfolding Energy - sRNA 5.71172 kcal/mol@LB@@LB@Position - mRNA 90 -- 130@LB@Position - sRNA 43 -- 87@LB@Position Seed - mRNA 114 -- 120@LB@Position Seed - sRNA 52 -- 58@LB@
129	0.00462	0.126	b1795	yeaQ	-13.29	0.014930	139 -- 150	70 -- 81	UPF0410 family protein		_____________138__________151\n_____________\|____________\|\n5'-AUA...CCGAU____________UUUUU...UCC-3'\n______________GUUGUGCUAUGC\n______________:\|\|\|\|\|\|\|\|\|\|\|\n______________UAACACGAUACG\n3'-UUU...UUAGU____________UCAUU...ACG-5'\n_____________\|____________\|\n_____________82___________69\n	144 -- 150	70 -- 76	-18.6071 kcal/mol	3.49189 kcal/mol	1.8201 kcal/mol	138 151@LB@ \| \|@LB@5'-AUA...CCGAU UUUUU...UCC-3'@LB@ GUUGUGCUAUGC@LB@ :\|\|\|\|\|\|\|\|\|\|\|@LB@ UAACACGAUACG@LB@3'-UUU...UUAGU UCAUU...ACG-5'@LB@ \| \|@LB@ 82 69@LB@@LB@@LB@Energy -13.29 kcal/mol@LB@Hybridization Energy -18.6071 kcal/mol@LB@Unfolding Energy - mRNA 3.49189 kcal/mol@LB@Unfolding Energy - sRNA 1.8201 kcal/mol@LB@@LB@Position - mRNA 139 -- 150@LB@Position - sRNA 70 -- 81@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 70 -- 76@LB@
130	0.00465	0.126	b2916	argP	-9.43	0.148863	238 -- 266	47 -- 73	transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor		_____________237___________________________267\n_____________\|_____________________________\|\n5'-GGC...ACUGG__________ACG____C_____UU____CGCGC...CAG-3'\n______________AUGCGGUGAU___UGAA_GAGGA__UGAG\n______________\|\|\|\|:\|\|:\|\|___::\|\|_:\|\|\|\|__\|:\|\|\n______________UACGUCAUUA___GUUU_UUCCU__AUUC\n3'-UUU...CACGA__________A______U_____UC____UGUUA...ACG-5'\n_____________\|_____________________________\|\n_____________74____________________________46\n	240 -- 246	65 -- 71	-19.9139 kcal/mol	5.97985 kcal/mol	4.50495 kcal/mol	237 267@LB@ \| \|@LB@5'-GGC...ACUGG ACG C UU CGCGC...CAG-3'@LB@ AUGCGGUGAU UGAA GAGGA UGAG@LB@ \|\|\|\|:\|\|:\|\| ::\|\| :\|\|\|\| \|:\|\|@LB@ UACGUCAUUA GUUU UUCCU AUUC@LB@3'-UUU...CACGA A U UC UGUUA...ACG-5'@LB@ \| \|@LB@ 74 46@LB@@LB@@LB@Energy -9.43 kcal/mol@LB@Hybridization Energy -19.9139 kcal/mol@LB@Unfolding Energy - mRNA 5.97985 kcal/mol@LB@Unfolding Energy - sRNA 4.50495 kcal/mol@LB@@LB@Position - mRNA 238 -- 266@LB@Position - sRNA 47 -- 73@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 65 -- 71@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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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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