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
151	0.01691	0.3749	b2442	intZ	-12.49	0.088679	278 -- 291	17 -- 31	CPZ-55 prophage; putative phage integrase	b2349	_____________277_________________292\n_____________\|___________________\|\n5'-ACA...AAACU____________C_G____CGGGG...UGC-3'\n______________CACCGAU__UCA_U_ACGC\n______________\|\|\|\|:\|\|__\|\|\|_\|_\|\|:\|\n______________GUGGUUA__AGU_A_UGUG\n3'-UUU...AAAAU_______UG___C_G____UACUA...UAG-5'\n_____________\|___________________\|\n_____________32__________________16\n	269 -- 275	180 -- 186	-14.1411 kcal/mol	1.5591 kcal/mol	4.88042 kcal/mol	277 292@LB@ \| \|@LB@5'-ACA...AAACU C G CGGGG...UGC-3'@LB@ CACCGAU UCA U ACGC@LB@ \|\|\|\|:\|\| \|\|\| \| \|\|:\|@LB@ GUGGUUA AGU A UGUG@LB@3'-UUU...AAAAU UG C G UACUA...UAG-5'@LB@ \| \|@LB@ 32 16@LB@@LB@@LB@Energy -12.49 kcal/mol@LB@Hybridization Energy -14.1411 kcal/mol@LB@Unfolding Energy - mRNA 1.5591 kcal/mol@LB@Unfolding Energy - sRNA 4.88042 kcal/mol@LB@@LB@Position - mRNA 278 -- 291@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 180 -- 186@LB@
177	0.02028	0.3833	b1732	katE	-12.45	0.090323	227 -- 246	168 -- 187	catalase HPII heme d-containing		_____________226___________________247\n_____________\|_____________________\|\n5'-UGG...AACCC_______C__________C__UACAC...ACG-3'\n______________ACAUCAG_AC_CAGUCAC_AC\n______________\|\|\|:\|\|:_\|\|_\|\|\|\|\|\|\|_\|\|\n______________UGUGGUU_UG_GUCAGUG_UG\n3'-UUU...UAAAA_______A__A__________UACUA...UAG-5'\n_____________\|_____________________\|\n_____________188___________________167\n	237 -- 243	170 -- 176	-19.9766 kcal/mol	1.23864 kcal/mol	4.88067 kcal/mol	226 247@LB@ \| \|@LB@5'-UGG...AACCC C C UACAC...ACG-3'@LB@ ACAUCAG AC CAGUCAC AC@LB@ \|\|\|:\|\|: \|\| \|\|\|\|\|\|\| \|\|@LB@ UGUGGUU UG GUCAGUG UG@LB@3'-UUU...UAAAA A A UACUA...UAG-5'@LB@ \| \|@LB@ 188 167@LB@@LB@@LB@Energy -12.45 kcal/mol@LB@Hybridization Energy -19.9766 kcal/mol@LB@Unfolding Energy - mRNA 1.23864 kcal/mol@LB@Unfolding Energy - sRNA 4.88067 kcal/mol@LB@@LB@Position - mRNA 227 -- 246@LB@Position - sRNA 168 -- 187@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 170 -- 176@LB@
10	0.0006004	0.1842	b3656	yicI	-12.42	0.091283	58 -- 101	169 -- 207	putative alpha-glucosidase		_____________57_________102\n_____________\|__________\|\n5'-ACA...GAUAA__________G-3'\n______________UGAAAUGGUG\n______________\|:\|\|\|\|:\|\|\|\n______________AUUUUAUCAC\n3'-UUU...GCGCC__________GACUA...UAG-5'\n_____________\|__________\|\n_____________208________168\n	293 -- 299	40 -- 46	-9.13222 kcal/mol	0.486237 kcal/mol	4.51378 kcal/mol	57 102@LB@ \| \|@LB@5'-ACA...GAUAA G-3'@LB@ UGAAAUGGUG@LB@ \|:\|\|\|\|:\|\|\|@LB@ AUUUUAUCAC@LB@3'-UUU...GCGCC GACUA...UAG-5'@LB@ \| \|@LB@ 208 168@LB@@LB@@LB@Energy -12.42 kcal/mol@LB@Hybridization Energy -9.13222 kcal/mol@LB@Unfolding Energy - mRNA 0.486237 kcal/mol@LB@Unfolding Energy - sRNA 4.51378 kcal/mol@LB@@LB@Position - mRNA 58 -- 101@LB@Position - sRNA 169 -- 207@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 40 -- 46@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@
88	0.009956	0.3575	b2672	ygaM	-12.38	0.093122	193 -- 231	56 -- 92	putative membrane-anchored DUF883 family ribosome-binding protein		_____________192______232\n_____________\|________\|\n5'-AAC...UGAAC________AGAAA...AGU-3'\n______________CUCAGUUA\n______________\|\|\|\|\|\|:\|\n______________GAGUCAGU\n3'-UUU...GUUAU________GUGUA...UAG-5'\n_____________\|________\|\n_____________93_______55\n	142 -- 148	171 -- 177	-10.1878 kcal/mol	1.87036 kcal/mol	0.207782 kcal/mol	192 232@LB@ \| \|@LB@5'-AAC...UGAAC AGAAA...AGU-3'@LB@ CUCAGUUA@LB@ \|\|\|\|\|\|:\|@LB@ GAGUCAGU@LB@3'-UUU...GUUAU GUGUA...UAG-5'@LB@ \| \|@LB@ 93 55@LB@@LB@@LB@Energy -12.38 kcal/mol@LB@Hybridization Energy -10.1878 kcal/mol@LB@Unfolding Energy - mRNA 1.87036 kcal/mol@LB@Unfolding Energy - sRNA 0.207782 kcal/mol@LB@@LB@Position - mRNA 193 -- 231@LB@Position - sRNA 56 -- 92@LB@Position Seed - mRNA 142 -- 148@LB@Position Seed - sRNA 171 -- 177@LB@
78	0.008099	0.3458	b2810	csdA	-12.29	0.097398	132 -- 155	3 -- 23	cysteine sulfinate desulfinase		_____________131_______________156\n_____________\|_________________\|\n5'-CUU...GGUUA____U________A___AAGUG...AAG-3'\n______________GCAC_CUCCUUGU_UCA\n______________\|\|\|\|_\|:\|\|\|\|\|:_\|\|\|\n______________CGUG_GGGGAACG_AGU\n3'-UUU...UACCC_____________A___AG-5'\n_____________\|_________________\|\n_____________24________________2\n	145 -- 151	7 -- 13	-20.4088 kcal/mol	3.04417 kcal/mol	7.17675 kcal/mol	131 156@LB@ \| \|@LB@5'-CUU...GGUUA U A AAGUG...AAG-3'@LB@ GCAC CUCCUUGU UCA@LB@ \|\|\|\| \|:\|\|\|\|\|: \|\|\|@LB@ CGUG GGGGAACG AGU@LB@3'-UUU...UACCC A AG-5'@LB@ \| \|@LB@ 24 2@LB@@LB@@LB@Energy -12.29 kcal/mol@LB@Hybridization Energy -20.4088 kcal/mol@LB@Unfolding Energy - mRNA 3.04417 kcal/mol@LB@Unfolding Energy - sRNA 7.17675 kcal/mol@LB@@LB@Position - mRNA 132 -- 155@LB@Position - sRNA 3 -- 23@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 7 -- 13@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@
20	0.001715	0.2633	b3453	ugpB	-12.22	0.100645	241 -- 257	18 -- 32	sn-glycerol-3-phosphate ABC transporter periplasmic binding protein		_____________240______________258\n_____________\|________________\|\n5'-UUC...AAUUC_____U__________AAGAG...UGG-3'\n______________GCGCA_UCGGUACAAC\n______________:\|\|\|\|_:\|:\|:\|\|\|\|\|\n______________UGCGU_GGUCGUGUUG\n3'-UUU...UUGGU_____U__________AAGCG...UAG-5'\n_____________\|________________\|\n_____________33_______________17\n	180 -- 186	63 -- 69	-22.0099 kcal/mol	5.49331 kcal/mol	9.84719 kcal/mol	240 258@LB@ \| \|@LB@5'-UUC...AAUUC U AAGAG...UGG-3'@LB@ GCGCA UCGGUACAAC@LB@ :\|\|\|\| :\|:\|:\|\|\|\|\|@LB@ UGCGU GGUCGUGUUG@LB@3'-UUU...UUGGU U AAGCG...UAG-5'@LB@ \| \|@LB@ 33 17@LB@@LB@@LB@Energy -12.22 kcal/mol@LB@Hybridization Energy -22.0099 kcal/mol@LB@Unfolding Energy - mRNA 5.49331 kcal/mol@LB@Unfolding Energy - sRNA 9.84719 kcal/mol@LB@@LB@Position - mRNA 241 -- 257@LB@Position - sRNA 18 -- 32@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 63 -- 69@LB@
200	0.02363	0.3833	b3068	mug	-12.10	0.106144	279 -- 297	1 -- 19	G/U mismatch-specific DNA glycosylase; xanthine DNA glycosylase		_____________278__________________298\n_____________\|____________________\|\n5'-UGG...GGACU___UU_______________CGG-3'\n______________GGU__UCCCUUUGCU_CAUC\n______________\|\|:__:\|\|\|:\|\|\|\|\|_\|\|\|\|\n______________CCG__GGGGGAACGA_GUAG\n3'-UUU...GUACC___U___________A____-5'\n_____________\|___________________\|\n_____________20__________________1\n	287 -- 293	6 -- 12	-22.9494 kcal/mol	3.41941 kcal/mol	8.43224 kcal/mol	278 298@LB@ \| \|@LB@5'-UGG...GGACU UU CGG-3'@LB@ GGU UCCCUUUGCU CAUC@LB@ \|\|: :\|\|\|:\|\|\|\|\| \|\|\|\|@LB@ CCG GGGGGAACGA GUAG@LB@3'-UUU...GUACC U A -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -12.10 kcal/mol@LB@Hybridization Energy -22.9494 kcal/mol@LB@Unfolding Energy - mRNA 3.41941 kcal/mol@LB@Unfolding Energy - sRNA 8.43224 kcal/mol@LB@@LB@Position - mRNA 279 -- 297@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 6 -- 12@LB@
131	0.01426	0.3575	b0048	folA	-12.08	0.107221	135 -- 211	115 -- 187	dihydrofolate reductase		_____________134_________212\n_____________\|___________\|\n5'-UCA...UUGUU___________GUAAU...GCA-3'\n______________UUUGUUUCAUU\n______________:\|\|\|:\|\|\|\|\|:\n______________GAACGAAGUAG\n3'-UUU...UGGGG___________-5'\n_____________\|__________\|\n_____________188________115\n	56 -- 62	1 -- 7	-10.5455 kcal/mol	1.7602 kcal/mol	1.03329 kcal/mol	134 212@LB@ \| \|@LB@5'-UCA...UUGUU GUAAU...GCA-3'@LB@ UUUGUUUCAUU@LB@ :\|\|\|:\|\|\|\|\|:@LB@ GAACGAAGUAG@LB@3'-UUU...UGGGG -5'@LB@ \| \|@LB@ 188 115@LB@@LB@@LB@Energy -12.08 kcal/mol@LB@Hybridization Energy -10.5455 kcal/mol@LB@Unfolding Energy - mRNA 1.7602 kcal/mol@LB@Unfolding Energy - sRNA 1.03329 kcal/mol@LB@@LB@Position - mRNA 135 -- 211@LB@Position - sRNA 115 -- 187@LB@Position Seed - mRNA 56 -- 62@LB@Position Seed - sRNA 1 -- 7@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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