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
28	0.0001471	0.01851	b0997	torA	-9.78	0.123932	184 -- 203	41 -- 60	trimethylamine N-oxide (TMAO) reductase I catalytic subunit	b3551 b1872	_____________183__________________204\n_____________\|____________________\|\n5'-UAC...GCGAU__________A__A______AACAA...CGC-3'\n______________AAGAAGGAAG_AA_AUAAUG\n______________\|\|:\|\|\|\|\|\|\|_\|\|_\|:\|\|\|:\n______________UUUUUCCUUC_UU_UGUUAU\n3'-UUU...UAAGU__________A__C______ACCUC...ACG-5'\n_____________\|____________________\|\n_____________61___________________40\n	187 -- 193	51 -- 57	-13.1224 kcal/mol	1.37417 kcal/mol	1.96633 kcal/mol	183 204@LB@ \| \|@LB@5'-UAC...GCGAU A A AACAA...CGC-3'@LB@ AAGAAGGAAG AA AUAAUG@LB@ \|\|:\|\|\|\|\|\|\| \|\| \|:\|\|\|:@LB@ UUUUUCCUUC UU UGUUAU@LB@3'-UUU...UAAGU A C ACCUC...ACG-5'@LB@ \| \|@LB@ 61 40@LB@@LB@@LB@Energy -9.78 kcal/mol@LB@Hybridization Energy -13.1224 kcal/mol@LB@Unfolding Energy - mRNA 1.37417 kcal/mol@LB@Unfolding Energy - sRNA 1.96633 kcal/mol@LB@@LB@Position - mRNA 184 -- 203@LB@Position - sRNA 41 -- 60@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 51 -- 57@LB@
199	0.008927	0.1548	b1019	efeB	-11.91	0.036296	188 -- 218	52 -- 88	deferrrochelatase periplasmic		_____________187___________________________________219\n_____________\|_____________________________________\|\n5'-GCC...GGGAC________GC______________________U____AACGG...CUC-3'\n______________UGGAUUAA____GUUAUGCAGUA___UAAAGA__GAA\n______________:\|:\|\|:\|\|____\|:\|\|\|\|\|\|\|\|\|___:\|\|\|:\|__\|\|\|\n______________GCUUAGUU____CGAUACGUCAU___GUUUUU__CUU\n3'-UUU...AGCAU________AACA___________UAA______UC___CAUUC...ACG-5'\n_____________\|_____________________________________\|\n_____________89____________________________________51\n	202 -- 208	66 -- 72	-22.4719 kcal/mol	5.89402 kcal/mol	4.66982 kcal/mol	187 219@LB@ \| \|@LB@5'-GCC...GGGAC GC U AACGG...CUC-3'@LB@ UGGAUUAA GUUAUGCAGUA UAAAGA GAA@LB@ :\|:\|\|:\|\| \|:\|\|\|\|\|\|\|\|\| :\|\|\|:\| \|\|\|@LB@ GCUUAGUU CGAUACGUCAU GUUUUU CUU@LB@3'-UUU...AGCAU AACA UAA UC CAUUC...ACG-5'@LB@ \| \|@LB@ 89 51@LB@@LB@@LB@Energy -11.91 kcal/mol@LB@Hybridization Energy -22.4719 kcal/mol@LB@Unfolding Energy - mRNA 5.89402 kcal/mol@LB@Unfolding Energy - sRNA 4.66982 kcal/mol@LB@@LB@Position - mRNA 188 -- 218@LB@Position - sRNA 52 -- 88@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 66 -- 72@LB@
174	0.007207	0.145	b1034	ycdX	-9.36	0.154134	94 -- 120	35 -- 63	alkaline phosphatase		_____________93_____________________________121\n_____________\|______________________________\|\n5'-GGC...CCAGC__________________G___C__C____AAGUC...AAC-3'\n______________UCGAAAAAGGG___GAGA_GGU_UG_GGGC\n______________\|\|:\|\|\|\|\|\|\|:___:\|\|\|_::\|_\|\|_\|:\|\|\n______________AGUUUUUUCCU___UUCU_UUA_AC_CUCG\n3'-UUU...CAUUA___________UCA____G___U_______CGUUG...ACG-5'\n_____________\|______________________________\|\n_____________64_____________________________34\n	98 -- 104	53 -- 59	-21.9855 kcal/mol	6.52956 kcal/mol	6.08557 kcal/mol	93 121@LB@ \| \|@LB@5'-GGC...CCAGC G C C AAGUC...AAC-3'@LB@ UCGAAAAAGGG GAGA GGU UG GGGC@LB@ \|\|:\|\|\|\|\|\|\|: :\|\|\| ::\| \|\| \|:\|\|@LB@ AGUUUUUUCCU UUCU UUA AC CUCG@LB@3'-UUU...CAUUA UCA G U CGUUG...ACG-5'@LB@ \| \|@LB@ 64 34@LB@@LB@@LB@Energy -9.36 kcal/mol@LB@Hybridization Energy -21.9855 kcal/mol@LB@Unfolding Energy - mRNA 6.52956 kcal/mol@LB@Unfolding Energy - sRNA 6.08557 kcal/mol@LB@@LB@Position - mRNA 94 -- 120@LB@Position - sRNA 35 -- 63@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 53 -- 59@LB@
91	0.002503	0.09689	b1062	pyrC	-7.37	0.386343	231 -- 263	1 -- 35	dihydro-orotase		_____________230_______________________________________264\n_____________\|_________________________________________\|\n5'-GCG...AGAUC_____________________ACUG___CC_______CC__GAUGG...CCA-3'\n______________CGC__CGCCCA______GACG____GCA__UUCACCU__GC\n______________\|\|\|__\|\|\|\|\|\|______\|\|\|\|____\|\|\|__\|\|\|\|\|\|\|__\|\|\n______________GCG__GCGGGU______CUGC____CGU__AAGUGGA__CG\n3'-UUU...ACCUC___UU______AGCGAA____AA__________________-5'\n_____________\|________________________________________\|\n_____________36_______________________________________1\n	253 -- 259	3 -- 9	-30.041 kcal/mol	7.38685 kcal/mol	15.286 kcal/mol	230 264@LB@ \| \|@LB@5'-GCG...AGAUC ACUG CC CC GAUGG...CCA-3'@LB@ CGC CGCCCA GACG GCA UUCACCU GC@LB@ \|\|\| \|\|\|\|\|\| \|\|\|\| \|\|\| \|\|\|\|\|\|\| \|\|@LB@ GCG GCGGGU CUGC CGU AAGUGGA CG@LB@3'-UUU...ACCUC UU AGCGAA AA -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -7.37 kcal/mol@LB@Hybridization Energy -30.041 kcal/mol@LB@Unfolding Energy - mRNA 7.38685 kcal/mol@LB@Unfolding Energy - sRNA 15.286 kcal/mol@LB@@LB@Position - mRNA 231 -- 263@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 3 -- 9@LB@
17	4.003e-05	0.007917	b1066	rimJ	-10.62	0.078044	194 -- 220	65 -- 91	ribosomal-protein-S5-alanine N-acetyltransferase		_____________193___________________________221\n_____________\|_____________________________\|\n5'-AUU...AGUAG____A____GU__________C_______CGUGC...AUU-3'\n______________GUAU_GAAU___UUG_GCUAU_GCAGUAA\n______________\|\|\|:_\|\|\|\|___\|\|\|_\|\|\|\|\|_\|\|\|\|\|\|\|\n______________CAUG_CUUA___AAC_CGAUA_CGUCAUU\n3'-UUU...CGCAG_________GUU___A_____________AAGUU...ACG-5'\n_____________\|_____________________________\|\n_____________92____________________________64\n	214 -- 220	65 -- 71	-21.0331 kcal/mol	5.8812 kcal/mol	4.53558 kcal/mol	193 221@LB@ \| \|@LB@5'-AUU...AGUAG A GU C CGUGC...AUU-3'@LB@ GUAU GAAU UUG GCUAU GCAGUAA@LB@ \|\|\|: \|\|\|\| \|\|\| \|\|\|\|\| \|\|\|\|\|\|\|@LB@ CAUG CUUA AAC CGAUA CGUCAUU@LB@3'-UUU...CGCAG GUU A AAGUU...ACG-5'@LB@ \| \|@LB@ 92 64@LB@@LB@@LB@Energy -10.62 kcal/mol@LB@Hybridization Energy -21.0331 kcal/mol@LB@Unfolding Energy - mRNA 5.8812 kcal/mol@LB@Unfolding Energy - sRNA 4.53558 kcal/mol@LB@@LB@Position - mRNA 194 -- 220@LB@Position - sRNA 65 -- 91@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 65 -- 71@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@
10	1.762e-05	0.005627	b1112	bhsA	-13.86	0.010205	165 -- 186	1 -- 22	biofilm cell surface and signaling protein	b0806 b0802	_____________164_____________________187\n_____________\|_______________________\|\n5'-UAA...UAAUU________AC_U___________AUAAG...AAC-3'\n______________GCUUG_CG__G_CAUUCAUCUGC\n______________\|\|\|\|\|_\|\|__\|_\|\|\|\|\|\|:\|\|\|\|\n______________CGAAC_GC__C_GUAAGUGGACG\n3'-UUU...GGUAG_____U__AA_____________-5'\n_____________\|______________________\|\n_____________23_____________________1\n	180 -- 186	1 -- 7	-25.8922 kcal/mol	3.94114 kcal/mol	8.09964 kcal/mol	164 187@LB@ \| \|@LB@5'-UAA...UAAUU AC U AUAAG...AAC-3'@LB@ GCUUG CG G CAUUCAUCUGC@LB@ \|\|\|\|\| \|\| \| \|\|\|\|\|\|:\|\|\|\|@LB@ CGAAC GC C GUAAGUGGACG@LB@3'-UUU...GGUAG U AA -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -13.86 kcal/mol@LB@Hybridization Energy -25.8922 kcal/mol@LB@Unfolding Energy - mRNA 3.94114 kcal/mol@LB@Unfolding Energy - sRNA 8.09964 kcal/mol@LB@@LB@Position - mRNA 165 -- 186@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 1 -- 7@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@
100	0.003303	0.1114	b1126	potA	-10.42	0.087379	73 -- 89	61 -- 76	spermidine/putrescine ABC transporter ATPase		_____________72________________90\n_____________\|_________________\|\n5'-CAA...AUAAA____A_C__________CAACA...UUC-3'\n______________GCUA_G_CAGUAAUUCA\n______________\|\|\|\|_\|_\|\|\|\|\|\|\|\|\|\|\n______________CGAU_C_GUCAUUAAGU\n3'-UUU...UAACA____A____________UUUUU...ACG-5'\n_____________\|_________________\|\n_____________77________________60\n	83 -- 89	61 -- 67	-17.6149 kcal/mol	3.71554 kcal/mol	3.47887 kcal/mol	72 90@LB@ \| \|@LB@5'-CAA...AUAAA A C CAACA...UUC-3'@LB@ GCUA G CAGUAAUUCA@LB@ \|\|\|\| \| \|\|\|\|\|\|\|\|\|\|@LB@ CGAU C GUCAUUAAGU@LB@3'-UUU...UAACA A UUUUU...ACG-5'@LB@ \| \|@LB@ 77 60@LB@@LB@@LB@Energy -10.42 kcal/mol@LB@Hybridization Energy -17.6149 kcal/mol@LB@Unfolding Energy - mRNA 3.71554 kcal/mol@LB@Unfolding Energy - sRNA 3.47887 kcal/mol@LB@@LB@Position - mRNA 73 -- 89@LB@Position - sRNA 61 -- 76@LB@Position Seed - mRNA 83 -- 89@LB@Position Seed - sRNA 61 -- 67@LB@
9	1.504e-05	0.005627	b1189	dadA	-11.44	0.048458	195 -- 226	48 -- 78	D-amino acid dehydrogenase		_____________194_______________________________227\n_____________\|_________________________________\|\n5'-CCG...UCGGA__G_______G___UG____UACU_________UGUGG...CGG-3'\n______________GU_GCUAUGC_AGU___UCA____GGGAAGUGG\n______________\|\|_\|\|\|\|\|\|\|_\|\|\|___\|\|\|____:\|\|\|\|\|\|::\n______________CA_CGAUACG_UCA___AGU____UCCUUCAUU\n3'-UUU...GUUAA______________UUA___UUUU_________CUGUU...ACG-5'\n_____________\|_________________________________\|\n_____________79________________________________47\n	220 -- 226	48 -- 54	-26.7579 kcal/mol	10.7545 kcal/mol	4.57065 kcal/mol	194 227@LB@ \| \|@LB@5'-CCG...UCGGA G G UG UACU UGUGG...CGG-3'@LB@ GU GCUAUGC AGU UCA GGGAAGUGG@LB@ \|\| \|\|\|\|\|\|\| \|\|\| \|\|\| :\|\|\|\|\|\|::@LB@ CA CGAUACG UCA AGU UCCUUCAUU@LB@3'-UUU...GUUAA UUA UUUU CUGUU...ACG-5'@LB@ \| \|@LB@ 79 47@LB@@LB@@LB@Energy -11.44 kcal/mol@LB@Hybridization Energy -26.7579 kcal/mol@LB@Unfolding Energy - mRNA 10.7545 kcal/mol@LB@Unfolding Energy - sRNA 4.57065 kcal/mol@LB@@LB@Position - mRNA 195 -- 226@LB@Position - sRNA 48 -- 78@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 48 -- 54@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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