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
199	0.02363	0.3833	b4141	yjeH	-8.04	0.585705	57 -- 67	64 -- 74	putative transporter	_____________56_____________68\n_____________\|______________\|\n5'-CAG...AAAUC___G_______C__AAAUU...CUG-3'\n______________UAC_CAGUUGC_CA\n______________\|\|\|_\|\|\|\|::\|_\|\|\n______________AUG_GUCAGUG_GU\n3'-UUU...UGGUU___A_______U__ACUAC...UAG-5'\n_____________\|______________\|\n_____________75_____________63\n	163 -- 169	170 -- 176	-11.2481 kcal/mol	2.09942 kcal/mol	0.433965 kcal/mol	56 68@LB@ \| \|@LB@5'-CAG...AAAUC G C AAAUU...CUG-3'@LB@ UAC CAGUUGC CA@LB@ \|\|\| \|\|\|\|::\| \|\|@LB@ AUG GUCAGUG GU@LB@3'-UUU...UGGUU A U ACUAC...UAG-5'@LB@ \| \|@LB@ 75 63@LB@@LB@@LB@Energy -8.04 kcal/mol@LB@Hybridization Energy -11.2481 kcal/mol@LB@Unfolding Energy - mRNA 2.09942 kcal/mol@LB@Unfolding Energy - sRNA 0.433965 kcal/mol@LB@@LB@Position - mRNA 57 -- 67@LB@Position - sRNA 64 -- 74@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 170 -- 176@LB@
195	0.02319	0.3833	b1233	ychJ	-7.86	0.620262	61 -- 80	1 -- 18	UPF0225 family protein	_____________60____________________________________81\n_____________\|_____________________________________\|\n5'-CUU...GCUAC_______________A___CUACU_____________ACGCC...UCA-3'\n______________UGCUCGGUUA_ACAU_GUG_____CAGGC_GGUUAAU\n______________\|:\|\|\|:\|\|:\|_\|\|\|\|_:\|\|_____\|\|\|\|\|_:\|\|:\|\|:\n______________AUGAGUCAGU_UGUA_UAC_____GUCCG_UCAGUUG\n3'-UUU...UGGUU__________G____C_____________U_______AAAGU...UAG-5'\n_____________\|_____________________________________\|\n_____________19____________________________________0\n	139 -- 145	171 -- 177	-29.0991 kcal/mol	9.80481 kcal/mol	8.18679 kcal/mol	60 81@LB@ \| \|@LB@5'-CUU...GCUAC A CUACU ACGCC...UCA-3'@LB@ UGCUCGGUUA ACAU GUG CAGGC GGUUAAU@LB@ \|:\|\|\|:\|\|:\| \|\|\|\| :\|\| \|\|\|\|\| :\|\|:\|\|:@LB@ AUGAGUCAGU UGUA UAC GUCCG UCAGUUG@LB@3'-UUU...UGGUU G C U AAAGU...UAG-5'@LB@ \| \|@LB@ 19 0@LB@@LB@@LB@Energy -7.86 kcal/mol@LB@Hybridization Energy -29.0991 kcal/mol@LB@Unfolding Energy - mRNA 9.80481 kcal/mol@LB@Unfolding Energy - sRNA 8.18679 kcal/mol@LB@@LB@Position - mRNA 61 -- 80@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 139 -- 145@LB@Position Seed - sRNA 171 -- 177@LB@
185	0.02128	0.3833	b2276	nuoN	-8.72	0.461673	62 -- 81	196 -- 211	NADH:ubiquinone oxidoreductase membrane subunit N	_____________61______________82\n_____________\|_______________\|\n5'-GUA...UAUGA__________U____GUGCU...AUC-3'\n______________UC_CUGUUGC_GGUG\n______________\|\|_\|\|\|\|:\|\|_\|\|\|:\n______________AG_GACAGCG_CCAU\n3'-UUU...GUUGA__C____________UUUAU...UAG-5'\n_____________\|_______________\|\n_____________212_____________195\n	69 -- 75	52 -- 58	-15.8669 kcal/mol	5.2118 kcal/mol	5.88061 kcal/mol	61 82@LB@ \| \|@LB@5'-GUA...UAUGA U GUGCU...AUC-3'@LB@ UC CUGUUGC GGUG@LB@ \|\| \|\|\|\|:\|\| \|\|\|:@LB@ AG GACAGCG CCAU@LB@3'-UUU...GUUGA C UUUAU...UAG-5'@LB@ \| \|@LB@ 212 195@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -15.8669 kcal/mol@LB@Unfolding Energy - mRNA 5.2118 kcal/mol@LB@Unfolding Energy - sRNA 5.88061 kcal/mol@LB@@LB@Position - mRNA 62 -- 81@LB@Position - sRNA 196 -- 211@LB@Position Seed - mRNA 69 -- 75@LB@Position Seed - sRNA 52 -- 58@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@
179	0.02059	0.3833	b2535	csiE	-10.55	0.216292	103 -- 142	58 -- 90	stationary phase inducible protein	_____________102___________143\n_____________\|_____________\|\n5'-GCA...GAUUA__________C__CAUUU...UGG-3'\n______________GCAUUCCCUU_GC\n______________\|\|\|::\|\|\|\|\|_\|\|\n______________CGUGGGGGAA_CG\n3'-UUU...UACCC_____________AAGUAG-5'\n_____________\|_____________\|\n_____________91____________57\n	133 -- 139	9 -- 15	-16.9052 kcal/mol	2.85301 kcal/mol	6.64496 kcal/mol	102 143@LB@ \| \|@LB@5'-GCA...GAUUA C CAUUU...UGG-3'@LB@ GCAUUCCCUU GC@LB@ \|\|\|::\|\|\|\|\| \|\|@LB@ CGUGGGGGAA CG@LB@3'-UUU...UACCC AAGUAG-5'@LB@ \| \|@LB@ 91 57@LB@@LB@@LB@Energy -10.55 kcal/mol@LB@Hybridization Energy -16.9052 kcal/mol@LB@Unfolding Energy - mRNA 2.85301 kcal/mol@LB@Unfolding Energy - sRNA 6.64496 kcal/mol@LB@@LB@Position - mRNA 103 -- 142@LB@Position - sRNA 58 -- 90@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 9 -- 15@LB@
183	0.02111	0.3833	b0461	tomB	-12.41	0.091700	125 -- 158	128 -- 160	Hha toxicity attenuator; conjugation-related protein	_____________124_________________________________________159\n_____________\|___________________________________________\|\n5'-UGC...GGAUG________CCCAAA_G_______AUC____C__C____G____UCUGU...AUC-3'\n______________AAUACUCA______A_ACAUGAU____GCA_AG_UUAA_UUUC\n______________\|\|\|\|\|\|\|\|______\|_\|\|\|\|\|\|\|____\|\|\|_\|\|_\|:\|\|_\|\|\|\|\n______________UUAUGAGU______U_UGUACUA____CGU_UC_AGUU_AAAG\n3'-UUU...UGUGG________CAG____G_______CGUC___________G____UCUUA...UAG-5'\n_____________\|___________________________________________\|\n_____________161_________________________________________127\n	224 -- 230	163 -- 169	-23.2008 kcal/mol	3.84731 kcal/mol	8.26055 kcal/mol	124 159@LB@ \| \|@LB@5'-UGC...GGAUG CCCAAA G AUC C C G UCUGU...AUC-3'@LB@ AAUACUCA A ACAUGAU GCA AG UUAA UUUC@LB@ \|\|\|\|\|\|\|\| \| \|\|\|\|\|\|\| \|\|\| \|\| \|:\|\| \|\|\|\|@LB@ UUAUGAGU U UGUACUA CGU UC AGUU AAAG@LB@3'-UUU...UGUGG CAG G CGUC G UCUUA...UAG-5'@LB@ \| \|@LB@ 161 127@LB@@LB@@LB@Energy -12.41 kcal/mol@LB@Hybridization Energy -23.2008 kcal/mol@LB@Unfolding Energy - mRNA 3.84731 kcal/mol@LB@Unfolding Energy - sRNA 8.26055 kcal/mol@LB@@LB@Position - mRNA 125 -- 158@LB@Position - sRNA 128 -- 160@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 163 -- 169@LB@
186	0.02152	0.3833	b3581	sgbH	-10.17	0.255482	135 -- 158	123 -- 153	3-keto-L-gulonate 6-phosphate decarboxylase	_____________134________159\n_____________\|__________\|\n5'-UUU...UAAGG__________UAUGA...AAG-3'\n______________AG_CACACAU\n______________\|\|_\|\|\|\|\|\|\|\n______________UC_GUGUGUA\n3'-UUU...AUGAG__A_______CUACG...UAG-5'\n_____________\|__________\|\n_____________154________122\n	193 -- 199	166 -- 172	-9.15702 kcal/mol	1.98532 kcal/mol	0.591348 kcal/mol	134 159@LB@ \| \|@LB@5'-UUU...UAAGG UAUGA...AAG-3'@LB@ AG CACACAU@LB@ \|\| \|\|\|\|\|\|\|@LB@ UC GUGUGUA@LB@3'-UUU...AUGAG A CUACG...UAG-5'@LB@ \| \|@LB@ 154 122@LB@@LB@@LB@Energy -10.17 kcal/mol@LB@Hybridization Energy -9.15702 kcal/mol@LB@Unfolding Energy - mRNA 1.98532 kcal/mol@LB@Unfolding Energy - sRNA 0.591348 kcal/mol@LB@@LB@Position - mRNA 135 -- 158@LB@Position - sRNA 123 -- 153@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 166 -- 172@LB@
184	0.02128	0.3833	b2831	mutH	-12.07	0.107608	142 -- 230	114 -- 189	methyl-directed mismatch repair protein	_____________141______________231\n_____________\|________________\|\n5'-UUC...CUGCG________________AUUGC...CGG-3'\n______________AAUAUUCGG_CACAUA\n______________\|\|\|\|:\|\|:\|_\|\|\|\|:\|\n______________UUAUGAGUC_GUGUGU\n3'-UUU...UGUGG_________A______ACUAC...UAG-5'\n_____________\|________________\|\n_____________190______________113\n	154 -- 160	174 -- 180	-15.1193 kcal/mol	2.199 kcal/mol	0.596263 kcal/mol	141 231@LB@ \| \|@LB@5'-UUC...CUGCG AUUGC...CGG-3'@LB@ AAUAUUCGG CACAUA@LB@ \|\|\|\|:\|\|:\| \|\|\|\|:\|@LB@ UUAUGAGUC GUGUGU@LB@3'-UUU...UGUGG A ACUAC...UAG-5'@LB@ \| \|@LB@ 190 113@LB@@LB@@LB@Energy -12.07 kcal/mol@LB@Hybridization Energy -15.1193 kcal/mol@LB@Unfolding Energy - mRNA 2.199 kcal/mol@LB@Unfolding Energy - sRNA 0.596263 kcal/mol@LB@@LB@Position - mRNA 142 -- 230@LB@Position - sRNA 114 -- 189@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 174 -- 180@LB@
178	0.02044	0.3833	b3433	asd	-8.72	0.462346	170 -- 185	58 -- 71	aspartate-semialdehyde dehydrogenase NAD(P)-binding	_____________169__________________186\n_____________\|____________________\|\n5'-UCA...UUAUA___________CUU______AAAAA...UCU-3'\n______________CAG_CACACAU___UGCAGG\n______________\|\|\|_\|\|\|\|\|\|\|___\|\|\|\|\|\|\n______________GUC_GUGUGUA___ACGUCC\n3'-UUU...UAUGA___A_______CU_______GUUCA...UAG-5'\n_____________\|____________________\|\n_____________72___________________57\n	173 -- 179	166 -- 172	-22.5694 kcal/mol	4.04779 kcal/mol	7.34152 kcal/mol	169 186@LB@ \| \|@LB@5'-UCA...UUAUA CUU AAAAA...UCU-3'@LB@ CAG CACACAU UGCAGG@LB@ \|\|\| \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ GUC GUGUGUA ACGUCC@LB@3'-UUU...UAUGA A CU GUUCA...UAG-5'@LB@ \| \|@LB@ 72 57@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -22.5694 kcal/mol@LB@Unfolding Energy - mRNA 4.04779 kcal/mol@LB@Unfolding Energy - sRNA 7.34152 kcal/mol@LB@@LB@Position - mRNA 170 -- 185@LB@Position - sRNA 58 -- 71@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 166 -- 172@LB@
190	0.02217	0.3833	b2754	ygbF	-10.33	0.238061	176 -- 225	124 -- 165	CRISPR adaptation ssRNA endonuclease	_____________175____________226\n_____________\|______________\|\n5'-UGG...AAAAU________GC____ACGAG...GUG-3'\n______________GUACCUCC__GCUU\n______________\|:\|\|\|:\|\|__\|\|\|\|\n______________CGUGGGGG__CGAA\n3'-UUU...UACCC________AA____GUAG-5'\n_____________\|______________\|\n_____________166____________123\n	232 -- 238	11 -- 17	-17.8256 kcal/mol	3.33543 kcal/mol	6.90657 kcal/mol	175 226@LB@ \| \|@LB@5'-UGG...AAAAU GC ACGAG...GUG-3'@LB@ GUACCUCC GCUU@LB@ \|:\|\|\|:\|\| \|\|\|\|@LB@ CGUGGGGG CGAA@LB@3'-UUU...UACCC AA GUAG-5'@LB@ \| \|@LB@ 166 123@LB@@LB@@LB@Energy -10.33 kcal/mol@LB@Hybridization Energy -17.8256 kcal/mol@LB@Unfolding Energy - mRNA 3.33543 kcal/mol@LB@Unfolding Energy - sRNA 6.90657 kcal/mol@LB@@LB@Position - mRNA 176 -- 225@LB@Position - sRNA 124 -- 165@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 11 -- 17@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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