Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
110	0.01217	0.3575	b1324	tpx	-10.54	0.217228	251 -- 258	126 -- 133	lipid hydroperoxide peroxidase		_____________250____________259\n_____________\|______________\|\n5'-GCG...ACUCC______________GUCUG...AAG-3'\n______________UUGUUGUCGCGGUG\n______________\|:\|:\|\|\|\|\|\|\|\|\|:\n______________AGCGACAGCGCCAU\n3'-UUU...GUUGA______________UUUAU...UAG-5'\n_____________\|______________\|\n_____________134____________125\n	99 -- 105	48 -- 54	-22.761 kcal/mol	7.03952 kcal/mol	5.88061 kcal/mol	250 259@LB@ \| \|@LB@5'-GCG...ACUCC GUCUG...AAG-3'@LB@ UUGUUGUCGCGGUG@LB@ \|:\|:\|\|\|\|\|\|\|\|\|:@LB@ AGCGACAGCGCCAU@LB@3'-UUU...GUUGA UUUAU...UAG-5'@LB@ \| \|@LB@ 134 125@LB@@LB@@LB@Energy -10.54 kcal/mol@LB@Hybridization Energy -22.761 kcal/mol@LB@Unfolding Energy - mRNA 7.03952 kcal/mol@LB@Unfolding Energy - sRNA 5.88061 kcal/mol@LB@@LB@Position - mRNA 251 -- 258@LB@Position - sRNA 126 -- 133@LB@Position Seed - mRNA 99 -- 105@LB@Position Seed - sRNA 48 -- 54@LB@
128	0.01397	0.3575	b2440	eutC	-11.59	0.134682	23 -- 48	126 -- 153	ethanolamine ammonia-lyase small subunit (light chain)		_____________22______________________________49\n_____________\|_______________________________\|\n______5'-CCGCU_______G_______________AC______GACCA...ACU-3'\n______________GGGUGAU___ACAUC_AUGCUCA__UAC_CA\n______________\|\|\|\|\|\|\|___\|\|\|:\|_\|\|:\|\|\|\|__:\|\|_\|\|\n______________CCCACUA___UGUGG_UAUGAGU__GUG_GU\n3'-UUU...GACCG_______AAA_____U_______CA___U__ACUAC...UAG-5'\n_____________\|_______________________________\|\n_____________154_____________________________125\n	19 -- 25	175 -- 181	-25.4577 kcal/mol	6.00586 kcal/mol	5.22711 kcal/mol	22 49@LB@ \| \|@LB@ 5'-CCGCU G AC GACCA...ACU-3'@LB@ GGGUGAU ACAUC AUGCUCA UAC CA@LB@ \|\|\|\|\|\|\| \|\|\|:\| \|\|:\|\|\|\| :\|\| \|\|@LB@ CCCACUA UGUGG UAUGAGU GUG GU@LB@3'-UUU...GACCG AAA U CA U ACUAC...UAG-5'@LB@ \| \|@LB@ 154 125@LB@@LB@@LB@Energy -11.59 kcal/mol@LB@Hybridization Energy -25.4577 kcal/mol@LB@Unfolding Energy - mRNA 6.00586 kcal/mol@LB@Unfolding Energy - sRNA 5.22711 kcal/mol@LB@@LB@Position - mRNA 23 -- 48@LB@Position - sRNA 126 -- 153@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 175 -- 181@LB@
192	0.02246	0.3833	b4340	yjiR	-11.68	0.128907	36 -- 62	126 -- 153	putative DNA-binding transcriptional regulator/putative aminotransferase		_____________35_______63\n_____________\|________\|\n5'-AGC...CAGAG________AUCCA...GUC-3'\n______________GCUUCAUC\n______________\|\|\|\|\|\|\|\|\n______________CGAAGUAG\n3'-UUU...GGGAA________-5'\n_____________\|_______\|\n_____________154_____126\n	50 -- 56	1 -- 7	-12.7164 kcal/mol	1.73081 kcal/mol	0.703102 kcal/mol	35 63@LB@ \| \|@LB@5'-AGC...CAGAG AUCCA...GUC-3'@LB@ GCUUCAUC@LB@ \|\|\|\|\|\|\|\|@LB@ CGAAGUAG@LB@3'-UUU...GGGAA -5'@LB@ \| \|@LB@ 154 126@LB@@LB@@LB@Energy -11.68 kcal/mol@LB@Hybridization Energy -12.7164 kcal/mol@LB@Unfolding Energy - mRNA 1.73081 kcal/mol@LB@Unfolding Energy - sRNA 0.703102 kcal/mol@LB@@LB@Position - mRNA 36 -- 62@LB@Position - sRNA 126 -- 153@LB@Position Seed - mRNA 50 -- 56@LB@Position Seed - sRNA 1 -- 7@LB@
86	0.009326	0.3575	b0899	ycaM	-11.50	0.140486	23 -- 68	127 -- 173	putative transporter		_____________22_______________________________________________________69\n_____________\|________________________________________________________\|\n5'-AGC...GAACU____GUU______UC_____UUUUUU___UCUU__A__U__C____U_________AAUUU...AUG-3'\n______________UACU___UCACAC____UGC______GUU____CU_UC_GA_UUGC__UUAUUCCA\n______________\|\|\|\|___\|\|\|\|\|\|____\|\|\|______\|\|:____\|\|_\|\|_\|\|_\|\|\|\|__\|:\|\|:\|\|\|\n______________AUGA___AGUGUG____ACG______CAG____GA_AG_CU_AACG__AGUAGGGU\n3'-UUU...UGGUU____GUC______UACU___UCCGUU___UU____A__U__U____CC________GACGU...UAG-5'\n_____________\|________________________________________________________\|\n_____________174______________________________________________________126\n	62 -- 68	127 -- 133	-29.7478 kcal/mol	2.56458 kcal/mol	15.6497 kcal/mol	22 69@LB@ \| \|@LB@5'-AGC...GAACU GUU UC UUUUUU UCUU A U C U AAUUU...AUG-3'@LB@ UACU UCACAC UGC GUU CU UC GA UUGC UUAUUCCA@LB@ \|\|\|\| \|\|\|\|\|\| \|\|\| \|\|: \|\| \|\| \|\| \|\|\|\| \|:\|\|:\|\|\|@LB@ AUGA AGUGUG ACG CAG GA AG CU AACG AGUAGGGU@LB@3'-UUU...UGGUU GUC UACU UCCGUU UU A U U CC GACGU...UAG-5'@LB@ \| \|@LB@ 174 126@LB@@LB@@LB@Energy -11.50 kcal/mol@LB@Hybridization Energy -29.7478 kcal/mol@LB@Unfolding Energy - mRNA 2.56458 kcal/mol@LB@Unfolding Energy - sRNA 15.6497 kcal/mol@LB@@LB@Position - mRNA 23 -- 68@LB@Position - sRNA 127 -- 173@LB@Position Seed - mRNA 62 -- 68@LB@Position Seed - sRNA 127 -- 133@LB@
34	0.002769	0.2736	b2416	ptsI	-14.05	0.042463	178 -- 225	128 -- 177	PEP-protein phosphotransferase of PTS system (enzyme I)		_____________177_________________________________________226\n_____________\|___________________________________________\|\n5'-GUG...AAAAA_________AGUAAGGUAGGGU______UU______UU_____AUCCC...CCG-3'\n______________UCAGUCACA_____________UAUGAU__CAGGCA__UUAGC\n______________\|\|\|\|\|\|\|\|\|_____________:\|\|\|\|\|__\|\|\|\|\|\|__\|:\|:\|\n______________AGUCAGUGU_____________GUACUA__GUCCGU__AGUUG\n3'-UUU...UUAUG____________________________C_______UC_____AAAGU...UAG-5'\n_____________\|___________________________________________\|\n_____________178_________________________________________127\n	180 -- 186	169 -- 175	-30.6202 kcal/mol	5.78851 kcal/mol	8.17404 kcal/mol	177 226@LB@ \| \|@LB@5'-GUG...AAAAA AGUAAGGUAGGGU UU UU AUCCC...CCG-3'@LB@ UCAGUCACA UAUGAU CAGGCA UUAGC@LB@ \|\|\|\|\|\|\|\|\| :\|\|\|\|\| \|\|\|\|\|\| \|:\|:\|@LB@ AGUCAGUGU GUACUA GUCCGU AGUUG@LB@3'-UUU...UUAUG C UC AAAGU...UAG-5'@LB@ \| \|@LB@ 178 127@LB@@LB@@LB@Energy -14.05 kcal/mol@LB@Hybridization Energy -30.6202 kcal/mol@LB@Unfolding Energy - mRNA 5.78851 kcal/mol@LB@Unfolding Energy - sRNA 8.17404 kcal/mol@LB@@LB@Position - mRNA 178 -- 225@LB@Position - sRNA 128 -- 177@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 169 -- 175@LB@
41	0.003653	0.2912	b2842	kduD	-13.01	0.069205	14 -- 50	128 -- 174	2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase; KDG oxidoreductase; 20-ketosteroid reductase	b4266 b2774	_____________13_______________________________________________51\n_____________\|________________________________________________\|\n5'-CCG...AACGC______U____________________GAG____________G_____CCCGA...CGG-3'\n______________GUCAUA_UGUGAUGCA_______UAAC___CAG____GCGGU_AUCUC\n______________\|\|\|\|:\|_::\|\|\|\|\|\|\|_______:\|\|\|___\|\|\|____\|\|\|\|\|_\|\|\|:\|\n______________CAGUGU_GUACUACGU_______GUUG___GUC____CGCCA_UAGGG\n3'-UUU...UGAGU________________CCGUUCA____AAA___UUAA_____G_____UGACG...UAG-5'\n_____________\|________________________________________________\|\n_____________175______________________________________________127\n	23 -- 29	160 -- 166	-35.8105 kcal/mol	9.71011 kcal/mol	15.5834 kcal/mol	13 51@LB@ \| \|@LB@5'-CCG...AACGC U GAG G CCCGA...CGG-3'@LB@ GUCAUA UGUGAUGCA UAAC CAG GCGGU AUCUC@LB@ \|\|\|\|:\| ::\|\|\|\|\|\|\| :\|\|\| \|\|\| \|\|\|\|\| \|\|\|:\|@LB@ CAGUGU GUACUACGU GUUG GUC CGCCA UAGGG@LB@3'-UUU...UGAGU CCGUUCA AAA UUAA G UGACG...UAG-5'@LB@ \| \|@LB@ 175 127@LB@@LB@@LB@Energy -13.01 kcal/mol@LB@Hybridization Energy -35.8105 kcal/mol@LB@Unfolding Energy - mRNA 9.71011 kcal/mol@LB@Unfolding Energy - sRNA 15.5834 kcal/mol@LB@@LB@Position - mRNA 14 -- 50@LB@Position - sRNA 128 -- 174@LB@Position Seed - mRNA 23 -- 29@LB@Position Seed - sRNA 160 -- 166@LB@
44	0.003817	0.292	b0967	rlmI	-10.41	0.230051	81 -- 118	128 -- 161	23S rRNA m(5)C1962 methyltransferase SAM-dependent		_____________80_________________________________119\n_____________\|__________________________________\|\n5'-CGU...UGAAC____C___AAACC_______UUAU_CA_______GACAU...AAG-3'\n______________UCGC_CGU_____CAGGCAA____G__GACUUUC\n______________\|\|:\|_\|:\|_____\|\|\|\|\|\|\|____\|__:\|\|\|\|\|\|\n______________AGUG_GUA_____GUCCGUU____C__UUGAAAG\n3'-UUU...GAGUC____U___CUAC_____________AG_______UCUUA...UAG-5'\n_____________\|__________________________________\|\n_____________162________________________________127\n	95 -- 101	145 -- 151	-21.0542 kcal/mol	5.99356 kcal/mol	7.97203 kcal/mol	80 119@LB@ \| \|@LB@5'-CGU...UGAAC C AAACC UUAU CA GACAU...AAG-3'@LB@ UCGC CGU CAGGCAA G GACUUUC@LB@ \|\|:\| \|:\| \|\|\|\|\|\|\| \| :\|\|\|\|\|\|@LB@ AGUG GUA GUCCGUU C UUGAAAG@LB@3'-UUU...GAGUC U CUAC AG UCUUA...UAG-5'@LB@ \| \|@LB@ 162 127@LB@@LB@@LB@Energy -10.41 kcal/mol@LB@Hybridization Energy -21.0542 kcal/mol@LB@Unfolding Energy - mRNA 5.99356 kcal/mol@LB@Unfolding Energy - sRNA 7.97203 kcal/mol@LB@@LB@Position - mRNA 81 -- 118@LB@Position - sRNA 128 -- 161@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 145 -- 151@LB@
145	0.01541	0.3575	b1191	cvrA	-14.91	0.028165	61 -- 91	128 -- 160	putative cation/proton antiporter		_____________60___________________________________92\n_____________\|____________________________________\|\n5'-UGA...CGGGA_____CUC_______GA___________________GUUCU...CUA-3'\n______________AGGCA___AGUUGAC__UUA_____GCGGUCAUCCU\n______________\|\|\|\|\|___\|\|\|::\|\|__\|:\|_____\|\|\|\|\|\|\|\|\|\|:\n______________UCCGU___UCAGUUG__AGU_____CGCCAGUAGGG\n3'-UUU...CUACG_______________AA___CUUAA___________UGACG...UAG-5'\n_____________\|____________________________________\|\n_____________161__________________________________127\n	85 -- 91	128 -- 134	-32.547 kcal/mol	9.03914 kcal/mol	12.2557 kcal/mol	60 92@LB@ \| \|@LB@5'-UGA...CGGGA CUC GA GUUCU...CUA-3'@LB@ AGGCA AGUUGAC UUA GCGGUCAUCCU@LB@ \|\|\|\|\| \|\|\|::\|\| \|:\| \|\|\|\|\|\|\|\|\|\|:@LB@ UCCGU UCAGUUG AGU CGCCAGUAGGG@LB@3'-UUU...CUACG AA CUUAA UGACG...UAG-5'@LB@ \| \|@LB@ 161 127@LB@@LB@@LB@Energy -14.91 kcal/mol@LB@Hybridization Energy -32.547 kcal/mol@LB@Unfolding Energy - mRNA 9.03914 kcal/mol@LB@Unfolding Energy - sRNA 12.2557 kcal/mol@LB@@LB@Position - mRNA 61 -- 91@LB@Position - sRNA 128 -- 160@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 128 -- 134@LB@
175	0.0199	0.3812	b3085	ygjP	-10.42	0.228945	225 -- 233	128 -- 136	putative metal dependent hydrolase		_____________224_______234\n_____________\|_________\|\n5'-AAC...UUCAG_________GAGCA...AAC-3'\n______________GGUUAUCCC\n______________\|\|\|:\|\|\|\|\|\n______________CCAGUAGGG\n3'-UUU...UAACG_________UGACG...UAG-5'\n_____________\|_________\|\n_____________137_______127\n	227 -- 233	128 -- 134	-15.1258 kcal/mol	2.43348 kcal/mol	4.55487 kcal/mol	224 234@LB@ \| \|@LB@5'-AAC...UUCAG GAGCA...AAC-3'@LB@ GGUUAUCCC@LB@ \|\|\|:\|\|\|\|\|@LB@ CCAGUAGGG@LB@3'-UUU...UAACG UGACG...UAG-5'@LB@ \| \|@LB@ 137 127@LB@@LB@@LB@Energy -10.42 kcal/mol@LB@Hybridization Energy -15.1258 kcal/mol@LB@Unfolding Energy - mRNA 2.43348 kcal/mol@LB@Unfolding Energy - sRNA 4.55487 kcal/mol@LB@@LB@Position - mRNA 225 -- 233@LB@Position - sRNA 128 -- 136@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 128 -- 134@LB@
180	0.02081	0.3833	b3728	pstS	-9.23	0.378852	18 -- 25	128 -- 135	phosphate ABC transporter periplasmic binding protein		_____________17___________26\n_____________\|____________\|\n5'-AGA...UCCUA____________GUAGC...GUG-3'\n______________UUUUGCUUC_UC\n______________::\|\|\|\|\|\|\|_\|\|\n______________GGAACGAAG_AG\n3'-UUU...GUGGG_________U__-5'\n_____________\|___________\|\n_____________136_________128\n	149 -- 155	4 -- 10	-10.5275 kcal/mol	1.71006 kcal/mol	1.04836 kcal/mol	17 26@LB@ \| \|@LB@5'-AGA...UCCUA GUAGC...GUG-3'@LB@ UUUUGCUUC UC@LB@ ::\|\|\|\|\|\|\| \|\|@LB@ GGAACGAAG AG@LB@3'-UUU...GUGGG U -5'@LB@ \| \|@LB@ 136 128@LB@@LB@@LB@Energy -9.23 kcal/mol@LB@Hybridization Energy -10.5275 kcal/mol@LB@Unfolding Energy - mRNA 1.71006 kcal/mol@LB@Unfolding Energy - sRNA 1.04836 kcal/mol@LB@@LB@Position - mRNA 18 -- 25@LB@Position - sRNA 128 -- 135@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 4 -- 10@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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