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
19	0.001698	0.2633	b2575	trmN	-12.50	0.088044	81 -- 92	14 -- 25	tRNA1(Val) (adenine(37)-N6)-methyltransferase	_____________80___________93\n_____________\|____________\|\n5'-ACC...UACAU__G_________GUAAU...GUA-3'\n______________CC_UGCUUCGUC\n______________\|\|_\|\|\|\|\|\|:\|\|\n______________GG_ACGAAGUAG\n3'-UUU...GUGGG__A_________-5'\n_____________\|___________\|\n_____________26__________14\n	222 -- 228	1 -- 7	-15.2724 kcal/mol	3.783 kcal/mol	1.04836 kcal/mol	80 93@LB@ \| \|@LB@5'-ACC...UACAU G GUAAU...GUA-3'@LB@ CC UGCUUCGUC@LB@ \|\| \|\|\|\|\|\|:\|\|@LB@ GG ACGAAGUAG@LB@3'-UUU...GUGGG A -5'@LB@ \| \|@LB@ 26 14@LB@@LB@@LB@Energy -12.50 kcal/mol@LB@Hybridization Energy -15.2724 kcal/mol@LB@Unfolding Energy - mRNA 3.783 kcal/mol@LB@Unfolding Energy - sRNA 1.04836 kcal/mol@LB@@LB@Position - mRNA 81 -- 92@LB@Position - sRNA 14 -- 25@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 1 -- 7@LB@
74	0.007724	0.3458	b1261	trpB	-16.40	0.014006	36 -- 47	195 -- 206	tryptophan synthase beta subunit	_____________35___________48\n_____________\|____________\|\n5'-UGG...AACGU____________GGGCU...UCA-3'\n______________UCUGCUGGCGGG\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________AGACGACCGCCC\n3'-UUU...AUAUU____________ACUAA...UAG-5'\n_____________\|____________\|\n_____________207__________194\n	41 -- 47	195 -- 201	-26.9412 kcal/mol	6.0368 kcal/mol	9.05854 kcal/mol	35 48@LB@ \| \|@LB@5'-UGG...AACGU GGGCU...UCA-3'@LB@ UCUGCUGGCGGG@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ AGACGACCGCCC@LB@3'-UUU...AUAUU ACUAA...UAG-5'@LB@ \| \|@LB@ 207 194@LB@@LB@@LB@Energy -16.40 kcal/mol@LB@Hybridization Energy -26.9412 kcal/mol@LB@Unfolding Energy - mRNA 6.0368 kcal/mol@LB@Unfolding Energy - sRNA 9.05854 kcal/mol@LB@@LB@Position - mRNA 36 -- 47@LB@Position - sRNA 195 -- 206@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 195 -- 201@LB@
96	0.01055	0.3575	b1953	yodD	-11.39	0.147949	264 -- 273	196 -- 205	uncharacterized protein	_____________263_____274\n_____________\|_______\|\n5'-CCA...UUCAC_______GUUUU...AAG-3'\n______________CUUCAUC\n______________\|\|\|\|\|\|\|\n______________GAAGUAG\n3'-UUU...GGAAC_______-5'\n_____________\|______\|\n_____________206____196\n	33 -- 39	1 -- 7	-8.82286 kcal/mol	0.690587 kcal/mol	0.701705 kcal/mol	263 274@LB@ \| \|@LB@5'-CCA...UUCAC GUUUU...AAG-3'@LB@ CUUCAUC@LB@ \|\|\|\|\|\|\|@LB@ GAAGUAG@LB@3'-UUU...GGAAC -5'@LB@ \| \|@LB@ 206 196@LB@@LB@@LB@Energy -11.39 kcal/mol@LB@Hybridization Energy -8.82286 kcal/mol@LB@Unfolding Energy - mRNA 0.690587 kcal/mol@LB@Unfolding Energy - sRNA 0.701705 kcal/mol@LB@@LB@Position - mRNA 264 -- 273@LB@Position - sRNA 196 -- 205@LB@Position Seed - mRNA 33 -- 39@LB@Position Seed - sRNA 1 -- 7@LB@
159	0.01779	0.3749	b2504	yfgG	-11.18	0.162405	230 -- 250	168 -- 187	uncharacterized protein	_____________229___________________251\n_____________\|_____________________\|\n5'-CCU...AAACG________UUAA_________GACCC...UUA-3'\n______________ACACCGAU____CAGUCGCAU\n______________\|\|\|\|\|:\|\|____\|\|\|\|\|:\|\|:\n______________UGUGGUUA____GUCAGUGUG\n3'-UUU...UAAAA________UGA__________UACUA...UAG-5'\n_____________\|_____________________\|\n_____________188___________________167\n	244 -- 250	168 -- 174	-22.7597 kcal/mol	5.28018 kcal/mol	4.88067 kcal/mol	229 251@LB@ \| \|@LB@5'-CCU...AAACG UUAA GACCC...UUA-3'@LB@ ACACCGAU CAGUCGCAU@LB@ \|\|\|\|\|:\|\| \|\|\|\|\|:\|\|:@LB@ UGUGGUUA GUCAGUGUG@LB@3'-UUU...UAAAA UGA UACUA...UAG-5'@LB@ \| \|@LB@ 188 167@LB@@LB@@LB@Energy -11.18 kcal/mol@LB@Hybridization Energy -22.7597 kcal/mol@LB@Unfolding Energy - mRNA 5.28018 kcal/mol@LB@Unfolding Energy - sRNA 4.88067 kcal/mol@LB@@LB@Position - mRNA 230 -- 250@LB@Position - sRNA 168 -- 187@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 168 -- 174@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@
18	0.001156	0.216	b3474	yhhT	-13.05	0.067927	149 -- 189	169 -- 204	UPF0118 family putative transporter	_____________148__________________________________________________________________190\n_____________\|____________________________________________________________________\|\n5'-GAC...GACGU____________UAAG____AGAAUAU________U_ACUCCCGC_____U______AAAA_______AGGAA...UCA-3'\n______________GAAAAUCAGCAG____AAUC_______UGCUGGCG_G________UACAC_UAAUAC____AGUCACA\n______________:\|\|\|\|:\|\|\|\|\|\|____\|\|\|\|_______\|\|\|\|\|\|\|\|_\|________\|\|\|\|\|_:\|\|\|\|\|____\|\|\|\|\|\|\|\n______________UUUUUGGUCGUC____UUAG_______ACGACCGC_C________AUGUG_GUUAUG____UCAGUGU\n________3'-UUU____________CAUA_____________________CACUAAA_____________AG_________GUACU...UAG-5'\n_____________\|____________________________________________________________________\|\n_____________205__________________________________________________________________168\n	183 -- 189	169 -- 175	-48.4478 kcal/mol	16.2259 kcal/mol	18.3074 kcal/mol	148 190@LB@ \| \|@LB@5'-GAC...GACGU UAAG AGAAUAU U ACUCCCGC U AAAA AGGAA...UCA-3'@LB@ GAAAAUCAGCAG AAUC UGCUGGCG G UACAC UAAUAC AGUCACA@LB@ :\|\|\|\|:\|\|\|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\| \| \|\|\|\|\| :\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UUUUUGGUCGUC UUAG ACGACCGC C AUGUG GUUAUG UCAGUGU@LB@ 3'-UUU CAUA CACUAAA AG GUACU...UAG-5'@LB@ \| \|@LB@ 205 168@LB@@LB@@LB@Energy -13.05 kcal/mol@LB@Hybridization Energy -48.4478 kcal/mol@LB@Unfolding Energy - mRNA 16.2259 kcal/mol@LB@Unfolding Energy - sRNA 18.3074 kcal/mol@LB@@LB@Position - mRNA 149 -- 189@LB@Position - sRNA 169 -- 204@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 169 -- 175@LB@
31	0.002426	0.2633	b2593	yfiH	-12.28	0.097562	144 -- 222	126 -- 203	UPF0124 family protein	_____________143___________________________________________________________________________223\n_____________\|_____________________________________________________________________________\|\n5'-CCA...AUUGA______GC______________AAGA_____AG_____________G____GG___U____AA__U_A_________AGUGG...CAC-3'\n______________GGUGAU___GCGCCGAU_UUCG____ACAUA__GAUG_____AAGU_GACU__UUA_GAGU__GC_G_UUGUCCCGC\n______________\|\|\|\|\|\|___:\|:\|\|:\|\|_:\|\|:____\|\|\|:\|__\|\|\|\|_____\|\|\|\|_:\|\|\|__\|:\|_\|\|:\|__\|\|_\|_\|::\|\|\|\|:\|\n______________CCACUA___UGUGGUUA_GAGU____UGUGU__CUAC_____UUCA_UUGA__AGU_CUUA__CG_C_AGUAGGGUG\n3'-UUU...ACCGC______AAA________U____CAG______A_____GUCCG____G____A_________A___C___________ACGUA...UAG-5'\n_____________\|_____________________________________________________________________________\|\n_____________204___________________________________________________________________________125\n	216 -- 222	126 -- 132	-51.0225 kcal/mol	17.9985 kcal/mol	20.5417 kcal/mol	143 223@LB@ \| \|@LB@5'-CCA...AUUGA GC AAGA AG G GG U AA U A AGUGG...CAC-3'@LB@ GGUGAU GCGCCGAU UUCG ACAUA GAUG AAGU GACU UUA GAGU GC G UUGUCCCGC@LB@ \|\|\|\|\|\| :\|:\|\|:\|\| :\|\|: \|\|\|:\| \|\|\|\| \|\|\|\| :\|\|\| \|:\| \|\|:\| \|\| \| \|::\|\|\|\|:\|@LB@ CCACUA UGUGGUUA GAGU UGUGU CUAC UUCA UUGA AGU CUUA CG C AGUAGGGUG@LB@3'-UUU...ACCGC AAA U CAG A GUCCG G A A C ACGUA...UAG-5'@LB@ \| \|@LB@ 204 125@LB@@LB@@LB@Energy -12.28 kcal/mol@LB@Hybridization Energy -51.0225 kcal/mol@LB@Unfolding Energy - mRNA 17.9985 kcal/mol@LB@Unfolding Energy - sRNA 20.5417 kcal/mol@LB@@LB@Position - mRNA 144 -- 222@LB@Position - sRNA 126 -- 203@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 126 -- 132@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@
113	0.01268	0.3575	b2066	udk	-9.33	0.364673	240 -- 253	17 -- 31	uridine/cytidine kinase	_____________239________________254\n_____________\|__________________\|\n5'-CGC...UUCGU_________C__AA____CAGGU...GUG-3'\n______________CGCCCCCUU_CU__CAUC\n______________\|:\|\|\|\|\|\|\|_\|\|__\|\|\|\|\n______________GUGGGGGAA_GA__GUAG\n3'-UUU...ACCCC_________C__A_____-5'\n_____________\|_________________\|\n_____________32________________17\n	161 -- 167	9 -- 15	-20.5437 kcal/mol	3.26859 kcal/mol	7.16879 kcal/mol	239 254@LB@ \| \|@LB@5'-CGC...UUCGU C AA CAGGU...GUG-3'@LB@ CGCCCCCUU CU CAUC@LB@ \|:\|\|\|\|\|\|\| \|\| \|\|\|\|@LB@ GUGGGGGAA GA GUAG@LB@3'-UUU...ACCCC C A -5'@LB@ \| \|@LB@ 32 17@LB@@LB@@LB@Energy -9.33 kcal/mol@LB@Hybridization Energy -20.5437 kcal/mol@LB@Unfolding Energy - mRNA 3.26859 kcal/mol@LB@Unfolding Energy - sRNA 7.16879 kcal/mol@LB@@LB@Position - mRNA 240 -- 253@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 9 -- 15@LB@
71	0.00726	0.3408	b2944	yggI	-9.32	0.365111	156 -- 174	1 -- 18	Zn-dependent metalloprotease-related protein	_____________155_____________175\n_____________\|_______________\|\n5'-GAA...AGCCA________AG_____UUUUC...ACC-3'\n______________CCUCUUGC__UCAUC\n______________\|\|:\|\|\|\|\|__\|\|\|\|\|\n______________GGGGAACG__AGUAG\n3'-UUU...CCGUG________A______-5'\n_____________\|______________\|\n_____________19_____________1\n	161 -- 167	7 -- 13	-18.0684 kcal/mol	1.30619 kcal/mol	6.71812 kcal/mol	155 175@LB@ \| \|@LB@5'-GAA...AGCCA AG UUUUC...ACC-3'@LB@ CCUCUUGC UCAUC@LB@ \|\|:\|\|\|\|\| \|\|\|\|\|@LB@ GGGGAACG AGUAG@LB@3'-UUU...CCGUG A -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -9.32 kcal/mol@LB@Hybridization Energy -18.0684 kcal/mol@LB@Unfolding Energy - mRNA 1.30619 kcal/mol@LB@Unfolding Energy - sRNA 6.71812 kcal/mol@LB@@LB@Position - mRNA 156 -- 174@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 7 -- 13@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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