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
163	0.01822	0.376	b1073	flgB	-9.73	0.308533	172 -- 220	24 -- 70	flagellar component of cell-proximal portion of basal-body rod	_____________171_______221\n_____________\|_________\|\n5'-UGA...AACAU_________CG-3'\n______________CGCCAAUGC\n______________\|:\|\|\|\|\|:\|\n______________GUGGUUAUG\n3'-UUU...AAAAU_________AGUCA...UAG-5'\n_____________\|_________\|\n_____________71________23\n	292 -- 298	178 -- 184	-11.5881 kcal/mol	1.63005 kcal/mol	3.31726 kcal/mol	171 221@LB@ \| \|@LB@5'-UGA...AACAU CG-3'@LB@ CGCCAAUGC@LB@ \|:\|\|\|\|\|:\|@LB@ GUGGUUAUG@LB@3'-UUU...AAAAU AGUCA...UAG-5'@LB@ \| \|@LB@ 71 23@LB@@LB@@LB@Energy -9.73 kcal/mol@LB@Hybridization Energy -11.5881 kcal/mol@LB@Unfolding Energy - mRNA 1.63005 kcal/mol@LB@Unfolding Energy - sRNA 3.31726 kcal/mol@LB@@LB@Position - mRNA 172 -- 220@LB@Position - sRNA 24 -- 70@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 178 -- 184@LB@
50	0.004849	0.3217	b1079	flgH	-12.97	0.070541	130 -- 141	23 -- 34	flagellar protein of basal-body outer-membrane L ring	_____________129____________________142\n_____________\|______________________\|\n5'-ACU...CGAUC__A_____CA____________ACUCU...GGG-3'\n______________AG_UGCUG__AAAACUGACGCA\n______________\|\|_\|\|\|\|\|__\|\|\|\|\|\|\|\|\|\|\|\|\n______________UC_ACGAC__UUUUGACUGCGU\n3'-UUU...UUUUA________UA____________ACCCC...UAG-5'\n_____________\|______________________\|\n_____________35_____________________22\n	135 -- 141	23 -- 29	-26.3449 kcal/mol	4.56982 kcal/mol	12.5314 kcal/mol	129 142@LB@ \| \|@LB@5'-ACU...CGAUC A CA ACUCU...GGG-3'@LB@ AG UGCUG AAAACUGACGCA@LB@ \|\| \|\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|@LB@ UC ACGAC UUUUGACUGCGU@LB@3'-UUU...UUUUA UA ACCCC...UAG-5'@LB@ \| \|@LB@ 35 22@LB@@LB@@LB@Energy -12.97 kcal/mol@LB@Hybridization Energy -26.3449 kcal/mol@LB@Unfolding Energy - mRNA 4.56982 kcal/mol@LB@Unfolding Energy - sRNA 12.5314 kcal/mol@LB@@LB@Position - mRNA 130 -- 141@LB@Position - sRNA 23 -- 34@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 23 -- 29@LB@
109	0.01201	0.3575	b1096	pabC	-8.08	0.578936	115 -- 139	144 -- 163	4-amino-4-deoxychorismate lyase component of para-aminobenzoate synthase multienzyme complex	_____________114____________140\n_____________\|______________\|\n5'-GUU...GUGUA_______CG_____GGUGG...ACG-3'\n______________ACUCCUU__GCUUC\n______________\|\|:\|\|:\|__\|\|\|\|\|\n______________UGGGGGA__CGAAG\n3'-UUU...CCCCG_______A______UAG-5'\n_____________\|______________\|\n_____________164____________143\n	29 -- 35	10 -- 16	-15.037 kcal/mol	0.971533 kcal/mol	6.96912 kcal/mol	114 140@LB@ \| \|@LB@5'-GUU...GUGUA CG GGUGG...ACG-3'@LB@ ACUCCUU GCUUC@LB@ \|\|:\|\|:\| \|\|\|\|\|@LB@ UGGGGGA CGAAG@LB@3'-UUU...CCCCG A UAG-5'@LB@ \| \|@LB@ 164 143@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -15.037 kcal/mol@LB@Unfolding Energy - mRNA 0.971533 kcal/mol@LB@Unfolding Energy - sRNA 6.96912 kcal/mol@LB@@LB@Position - mRNA 115 -- 139@LB@Position - sRNA 144 -- 163@LB@Position Seed - mRNA 29 -- 35@LB@Position Seed - sRNA 10 -- 16@LB@
12	0.0007005	0.1842	b1101	ptsG	-16.86	0.011310	173 -- 192	168 -- 187	fused glucose-specific PTS enzymes: IIB component/IIC component	_____________172__________________193\n_____________\|____________________\|\n5'-CAU...AAAAA_____C________GA____UCUCA...GUU-3'\n______________GCACC_AUACUCAG__GCAC\n______________:\|\|\|\|_\|\|\|\|\|\|\|\|__:\|\|\|\n______________UGUGG_UAUGAGUC__UGUG\n3'-UUU...UAAAA_____U________AG____UACUA...UAG-5'\n_____________\|____________________\|\n_____________188__________________167\n	180 -- 186	174 -- 180	-27.3381 kcal/mol	3.90127 kcal/mol	4.88067 kcal/mol	172 193@LB@ \| \|@LB@5'-CAU...AAAAA C GA UCUCA...GUU-3'@LB@ GCACC AUACUCAG GCAC@LB@ :\|\|\|\| \|\|\|\|\|\|\|\| :\|\|\|@LB@ UGUGG UAUGAGUC UGUG@LB@3'-UUU...UAAAA U AG UACUA...UAG-5'@LB@ \| \|@LB@ 188 167@LB@@LB@@LB@Energy -16.86 kcal/mol@LB@Hybridization Energy -27.3381 kcal/mol@LB@Unfolding Energy - mRNA 3.90127 kcal/mol@LB@Unfolding Energy - sRNA 4.88067 kcal/mol@LB@@LB@Position - mRNA 173 -- 192@LB@Position - sRNA 168 -- 187@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 174 -- 180@LB@
198	0.0236	0.3833	b1110	ycfJ	-10.00	0.275196	69 -- 84	142 -- 161	uncharacterized protein	_____________68__________________85\n_____________\|___________________\|\n5'-ACU...CCAGC_______GC___UU_____UUCUG...AAU-3'\n______________CAUUCCC__GCU__UCAUC\n______________\|\|::\|\|\|__\|\|\|__\|\|\|\|\|\n______________GUGGGGG__CGA__AGUAG\n3'-UUU...ACCCC_______AA__________-5'\n_____________\|__________________\|\n_____________162________________142\n	113 -- 119	11 -- 17	-18.8572 kcal/mol	2.50144 kcal/mol	7.16879 kcal/mol	68 85@LB@ \| \|@LB@5'-ACU...CCAGC GC UU UUCUG...AAU-3'@LB@ CAUUCCC GCU UCAUC@LB@ \|\|::\|\|\| \|\|\| \|\|\|\|\|@LB@ GUGGGGG CGA AGUAG@LB@3'-UUU...ACCCC AA -5'@LB@ \| \|@LB@ 162 142@LB@@LB@@LB@Energy -10.00 kcal/mol@LB@Hybridization Energy -18.8572 kcal/mol@LB@Unfolding Energy - mRNA 2.50144 kcal/mol@LB@Unfolding Energy - sRNA 7.16879 kcal/mol@LB@@LB@Position - mRNA 69 -- 84@LB@Position - sRNA 142 -- 161@LB@Position Seed - mRNA 113 -- 119@LB@Position Seed - sRNA 11 -- 17@LB@
28	0.002284	0.2633	b1114	mfd	-18.81	0.004608	253 -- 297	50 -- 95	transcription-repair coupling factor	_____________252______________298\n_____________\|________________\|\n5'-UUC...GCGUC___U____________CGGCG...AAA-3'\n______________UGC_GGGCGAGUUAAC\n______________\|\|\|_:\|\|\|:\|\|\|:\|\|\|\n______________ACG_UCCGUUCAGUUG\n3'-UUU...GUACU________________AAAGU...UAG-5'\n_____________\|________________\|\n_____________96_______________49\n	262 -- 268	149 -- 155	-20.6961 kcal/mol	4.60584 kcal/mol	7.12854 kcal/mol	252 298@LB@ \| \|@LB@5'-UUC...GCGUC U CGGCG...AAA-3'@LB@ UGC GGGCGAGUUAAC@LB@ \|\|\| :\|\|\|:\|\|\|:\|\|\|@LB@ ACG UCCGUUCAGUUG@LB@3'-UUU...GUACU AAAGU...UAG-5'@LB@ \| \|@LB@ 96 49@LB@@LB@@LB@Energy -18.81 kcal/mol@LB@Hybridization Energy -20.6961 kcal/mol@LB@Unfolding Energy - mRNA 4.60584 kcal/mol@LB@Unfolding Energy - sRNA 7.12854 kcal/mol@LB@@LB@Position - mRNA 253 -- 297@LB@Position - sRNA 50 -- 95@LB@Position Seed - mRNA 262 -- 268@LB@Position Seed - sRNA 149 -- 155@LB@
120	0.01317	0.3575	b1158	pinE	-11.56	0.136715	30 -- 59	115 -- 145	e14 prophage; site-specific DNA recombinase	_____________29_____________________60\n_____________\|______________________\|\n5'-AGC...CCGGG______________GUA_____GAGCC...ACA-3'\n______________ACACCAA____CAG___AUGCA\n______________\|\|\|\|\|\|\|____\|\|\|___\|::\|\|\n______________UGUGGUU____GUC___UGUGU\n3'-UUU...UAAAA_______AUGA___AG______ACUAC...UAG-5'\n_____________\|______________________\|\n_____________146____________________114\n	98 -- 104	181 -- 187	-13.8739 kcal/mol	4.34554 kcal/mol	5.05492 kcal/mol	29 60@LB@ \| \|@LB@5'-AGC...CCGGG GUA GAGCC...ACA-3'@LB@ ACACCAA CAG AUGCA@LB@ \|\|\|\|\|\|\| \|\|\| \|::\|\|@LB@ UGUGGUU GUC UGUGU@LB@3'-UUU...UAAAA AUGA AG ACUAC...UAG-5'@LB@ \| \|@LB@ 146 114@LB@@LB@@LB@Energy -11.56 kcal/mol@LB@Hybridization Energy -13.8739 kcal/mol@LB@Unfolding Energy - mRNA 4.34554 kcal/mol@LB@Unfolding Energy - sRNA 5.05492 kcal/mol@LB@@LB@Position - mRNA 30 -- 59@LB@Position - sRNA 115 -- 145@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 181 -- 187@LB@
158	0.01775	0.3749	b1187	fadR	-13.89	0.045798	42 -- 66	152 -- 176	fatty acid metabolism regulon transcriptional regulator	_____________41________________________67\n_____________\|_________________________\|\n5'-AAA...CUUAA______G___G__GUG_________UUGAU...CAG-3'\n______________CGGUCA_GCA_GA___AGGCAAGUC\n______________\|:\|\|\|\|_:\|\|_\|\|___\|\|\|\|\|\|\|\|\|\n______________GUCAGU_UGU_CU___UCCGUUCAG\n3'-UUU...UAUGA______G___A__ACG_________UUGAA...UAG-5'\n_____________\|_________________________\|\n_____________177_______________________151\n	60 -- 66	152 -- 158	-31.5031 kcal/mol	7.04431 kcal/mol	8.02398 kcal/mol	41 67@LB@ \| \|@LB@5'-AAA...CUUAA G G GUG UUGAU...CAG-3'@LB@ CGGUCA GCA GA AGGCAAGUC@LB@ \|:\|\|\|\| :\|\| \|\| \|\|\|\|\|\|\|\|\|@LB@ GUCAGU UGU CU UCCGUUCAG@LB@3'-UUU...UAUGA G A ACG UUGAA...UAG-5'@LB@ \| \|@LB@ 177 151@LB@@LB@@LB@Energy -13.89 kcal/mol@LB@Hybridization Energy -31.5031 kcal/mol@LB@Unfolding Energy - mRNA 7.04431 kcal/mol@LB@Unfolding Energy - sRNA 8.02398 kcal/mol@LB@@LB@Position - mRNA 42 -- 66@LB@Position - sRNA 152 -- 176@LB@Position Seed - mRNA 60 -- 66@LB@Position Seed - sRNA 152 -- 158@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@
87	0.009479	0.3575	b1192	ldcA	-9.25	0.375459	184 -- 216	125 -- 154	murein tetrapeptide carboxypeptidase; LD-carboxypeptidase A	_____________183_______________217\n_____________\|_________________\|\n5'-UGC...AGCAC__CG_____________UCCAG...UCA-3'\n______________GC__CGCUG_CGUGGUA\n______________:\|__\|\|\|\|\|_\|\|:\|\|\|\|\n______________UG__GCGAC_GCGCCAU\n3'-UUU...CGUGU__AA_____A_______UUUAU...UAG-5'\n_____________\|_________________\|\n_____________155_______________124\n	261 -- 267	48 -- 54	-20.6657 kcal/mol	8.36057 kcal/mol	6.14531 kcal/mol	183 217@LB@ \| \|@LB@5'-UGC...AGCAC CG UCCAG...UCA-3'@LB@ GC CGCUG CGUGGUA@LB@ :\| \|\|\|\|\| \|\|:\|\|\|\|@LB@ UG GCGAC GCGCCAU@LB@3'-UUU...CGUGU AA A UUUAU...UAG-5'@LB@ \| \|@LB@ 155 124@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -20.6657 kcal/mol@LB@Unfolding Energy - mRNA 8.36057 kcal/mol@LB@Unfolding Energy - sRNA 6.14531 kcal/mol@LB@@LB@Position - mRNA 184 -- 216@LB@Position - sRNA 125 -- 154@LB@Position Seed - mRNA 261 -- 267@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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