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
187	0.02173	0.3833	b3679	yidK	-10.16	0.256396	240 -- 256	191 -- 205	putative transporter	_____________239________________________________________257\n_____________\|__________________________________________\|\n5'-UUU...UUACG_________GC______________U____GAA_________AAACA...AAG-3'\n______________CUGCUGGUG__GGUGAU____CACC_GGUG___GGUC_CGCA\n______________\|\|\|\|\|\|\|:\|__\|\|\|\|\|\|____\|\|\|\|_::\|:___:\|\|\|_\|:\|\|\n______________GACGACCGC__CCACUA____GUGG_UUAU___UCAG_GUGU\n3'-UUU...UAUUA_________________AAAU_________GAG____U____ACUAC...UAG-5'\n_____________\|__________________________________________\|\n_____________206________________________________________190\n	242 -- 248	197 -- 203	-39.2862 kcal/mol	16.885 kcal/mol	15.3993 kcal/mol	239 257@LB@ \| \|@LB@5'-UUU...UUACG GC U GAA AAACA...AAG-3'@LB@ CUGCUGGUG GGUGAU CACC GGUG GGUC CGCA@LB@ \|\|\|\|\|\|\|:\| \|\|\|\|\|\| \|\|\|\| ::\|: :\|\|\| \|:\|\|@LB@ GACGACCGC CCACUA GUGG UUAU UCAG GUGU@LB@3'-UUU...UAUUA AAAU GAG U ACUAC...UAG-5'@LB@ \| \|@LB@ 206 190@LB@@LB@@LB@Energy -10.16 kcal/mol@LB@Hybridization Energy -39.2862 kcal/mol@LB@Unfolding Energy - mRNA 16.885 kcal/mol@LB@Unfolding Energy - sRNA 15.3993 kcal/mol@LB@@LB@Position - mRNA 240 -- 256@LB@Position - sRNA 191 -- 205@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 197 -- 203@LB@
82	0.008839	0.3575	b3680	yidL	-8.33	0.532337	91 -- 113	142 -- 164	AraC family putative transcriptional regulator	_____________90________________114\n_____________\|_________________\|\n5'-AAC...UGCGU________GCAG_____UUCUU...UGA-3'\n______________CGGGUCAG____UCAGA\n______________\|::\|\|\|\|:____\|\|\|\|\|\n______________GUUCAGUU____AGUCU\n3'-UUU...CGUCC________GAA______UAACG...UAG-5'\n_____________\|_________________\|\n_____________165_______________141\n	97 -- 103	151 -- 157	-14.3717 kcal/mol	4.36777 kcal/mol	4.37859 kcal/mol	90 114@LB@ \| \|@LB@5'-AAC...UGCGU GCAG UUCUU...UGA-3'@LB@ CGGGUCAG UCAGA@LB@ \|::\|\|\|\|: \|\|\|\|\|@LB@ GUUCAGUU AGUCU@LB@3'-UUU...CGUCC GAA UAACG...UAG-5'@LB@ \| \|@LB@ 165 141@LB@@LB@@LB@Energy -8.33 kcal/mol@LB@Hybridization Energy -14.3717 kcal/mol@LB@Unfolding Energy - mRNA 4.36777 kcal/mol@LB@Unfolding Energy - sRNA 4.37859 kcal/mol@LB@@LB@Position - mRNA 91 -- 113@LB@Position - sRNA 142 -- 164@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 151 -- 157@LB@
171	0.01954	0.3812	b3687	ibpA	-6.40	0.875621	11 -- 20	10 -- 18	heat shock chaperone	_____________10____________21\n_____________\|_____________\|\n5'-AAC...GCCCC_______U_____AUAGA...GCU-3'\n______________CUCAGUC_AUGCA\n______________\|\|\|\|\|\|\|_\|::\|\|\n______________GAGUCAG_UGUGU\n3'-UUU...GUUAU_____________ACUAC...UAG-5'\n_____________\|_____________\|\n_____________19____________9\n	19 -- 25	172 -- 178	-14.2159 kcal/mol	5.36362 kcal/mol	0.433674 kcal/mol	10 21@LB@ \| \|@LB@5'-AAC...GCCCC U AUAGA...GCU-3'@LB@ CUCAGUC AUGCA@LB@ \|\|\|\|\|\|\| \|::\|\|@LB@ GAGUCAG UGUGU@LB@3'-UUU...GUUAU ACUAC...UAG-5'@LB@ \| \|@LB@ 19 9@LB@@LB@@LB@Energy -6.40 kcal/mol@LB@Hybridization Energy -14.2159 kcal/mol@LB@Unfolding Energy - mRNA 5.36362 kcal/mol@LB@Unfolding Energy - sRNA 0.433674 kcal/mol@LB@@LB@Position - mRNA 11 -- 20@LB@Position - sRNA 10 -- 18@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 172 -- 178@LB@
154	0.01719	0.3749	b3726	pstA	-9.04	0.409183	290 -- 297	24 -- 31	phosphate ABC transporter permease	_____________289____________298\n_____________\|______________\|\n5'-CAG...CCGUA_________C____U-3'\n______________UUGCGCUGA_GCUC\n______________\|\|:\|:\|::\|_:\|\|\|\n______________AAUGUGGUU_UGAG\n3'-UUU...ACUAA_________A____UCAGU...UAG-5'\n_____________\|______________\|\n_____________32_____________23\n	288 -- 294	181 -- 187	-13.2096 kcal/mol	2.6708 kcal/mol	3.40409 kcal/mol	289 298@LB@ \| \|@LB@5'-CAG...CCGUA C U-3'@LB@ UUGCGCUGA GCUC@LB@ \|\|:\|:\|::\| :\|\|\|@LB@ AAUGUGGUU UGAG@LB@3'-UUU...ACUAA A UCAGU...UAG-5'@LB@ \| \|@LB@ 32 23@LB@@LB@@LB@Energy -9.04 kcal/mol@LB@Hybridization Energy -13.2096 kcal/mol@LB@Unfolding Energy - mRNA 2.6708 kcal/mol@LB@Unfolding Energy - sRNA 3.40409 kcal/mol@LB@@LB@Position - mRNA 290 -- 297@LB@Position - sRNA 24 -- 31@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 181 -- 187@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@
63	0.006154	0.3261	b3750	rbsC	-15.65	0.019915	89 -- 120	139 -- 174	D-ribose ABC transporter permease	_____________88___________________________________121\n_____________\|____________________________________\|\n5'-GAU...UCAUC___________A_______UC_____GG________UACUC...UCU-3'\n______________GUCAUGCAUGA___GGGCA__UCAGC____GGAAUU\n______________\|\|\|\|::\|\|\|\|\|___:\|\|\|\|__\|\|\|:\|____:\|\|\|\|\|\n______________CAGUGUGUACU___UCCGU__AGUUG____UCUUAA\n3'-UUU...UGAGU___________ACG_____UC_____AAAG______CGCCA...UAG-5'\n_____________\|____________________________________\|\n_____________175__________________________________138\n	91 -- 97	166 -- 172	-33.4294 kcal/mol	9.19626 kcal/mol	8.8011 kcal/mol	88 121@LB@ \| \|@LB@5'-GAU...UCAUC A UC GG UACUC...UCU-3'@LB@ GUCAUGCAUGA GGGCA UCAGC GGAAUU@LB@ \|\|\|\|::\|\|\|\|\| :\|\|\|\| \|\|\|:\| :\|\|\|\|\|@LB@ CAGUGUGUACU UCCGU AGUUG UCUUAA@LB@3'-UUU...UGAGU ACG UC AAAG CGCCA...UAG-5'@LB@ \| \|@LB@ 175 138@LB@@LB@@LB@Energy -15.65 kcal/mol@LB@Hybridization Energy -33.4294 kcal/mol@LB@Unfolding Energy - mRNA 9.19626 kcal/mol@LB@Unfolding Energy - sRNA 8.8011 kcal/mol@LB@@LB@Position - mRNA 89 -- 120@LB@Position - sRNA 139 -- 174@LB@Position Seed - mRNA 91 -- 97@LB@Position Seed - sRNA 166 -- 172@LB@
193	0.0225	0.3833	b3751	rbsB	-14.76	0.030308	38 -- 56	74 -- 93	D-ribose ABC transporter periplasmic binding protein; ribose chemotaxis receptor	_____________37________________________________________________57\n_____________\|_________________________________________________\|\n___5'-GCGGUACG_____GG______GAAAA_____CA___U____________________UUAAU...UCU-3'\n______________AGUCU__CGGGCG_____GGUCG__UUG_UGGGACGUU_GAUCGGCGCA\n______________\|\|\|\|:__\|::\|\|:_____::\|\|\|__\|\|\|_\|\|\|\|\|\|\|:\|_:\|:\|::\|\|\|\|\n______________UCAGG__GUUCGU_____UUAGC__AAC_ACCCUGCGA_UUGGUUGCGU\n3'-UUU...CGUAG_____AA______ACCAA____________________A__________UGGUC...UAG-5'\n_____________\|_________________________________________________\|\n_____________94________________________________________________73\n	40 -- 46	85 -- 91	-47.7546 kcal/mol	17.619 kcal/mol	19.1533 kcal/mol	37 57@LB@ \| \|@LB@ 5'-GCGGUACG GG GAAAA CA U UUAAU...UCU-3'@LB@ AGUCU CGGGCG GGUCG UUG UGGGACGUU GAUCGGCGCA@LB@ \|\|\|\|: \|::\|\|: ::\|\|\| \|\|\| \|\|\|\|\|\|\|:\| :\|:\|::\|\|\|\|@LB@ UCAGG GUUCGU UUAGC AAC ACCCUGCGA UUGGUUGCGU@LB@3'-UUU...CGUAG AA ACCAA A UGGUC...UAG-5'@LB@ \| \|@LB@ 94 73@LB@@LB@@LB@Energy -14.76 kcal/mol@LB@Hybridization Energy -47.7546 kcal/mol@LB@Unfolding Energy - mRNA 17.619 kcal/mol@LB@Unfolding Energy - sRNA 19.1533 kcal/mol@LB@@LB@Position - mRNA 38 -- 56@LB@Position - sRNA 74 -- 93@LB@Position Seed - mRNA 40 -- 46@LB@Position Seed - sRNA 85 -- 91@LB@
138	0.01487	0.3575	b3771	ilvD	-15.83	0.018324	35 -- 66	67 -- 98	dihydroxyacid dehydratase	_____________34______67\n_____________\|_______\|\n5'-GCG...AAAAA_______GCACG...GUA-3'\n______________UGGGACG\n______________\|\|\|\|\|\|\|\n______________ACCCUGC\n3'-UUU...GCAAC_______GAAUU...UAG-5'\n_____________\|_______\|\n_____________99______66\n	147 -- 153	87 -- 93	-12.7493 kcal/mol	2.26202 kcal/mol	4.21173 kcal/mol	34 67@LB@ \| \|@LB@5'-GCG...AAAAA GCACG...GUA-3'@LB@ UGGGACG@LB@ \|\|\|\|\|\|\|@LB@ ACCCUGC@LB@3'-UUU...GCAAC GAAUU...UAG-5'@LB@ \| \|@LB@ 99 66@LB@@LB@@LB@Energy -15.83 kcal/mol@LB@Hybridization Energy -12.7493 kcal/mol@LB@Unfolding Energy - mRNA 2.26202 kcal/mol@LB@Unfolding Energy - sRNA 4.21173 kcal/mol@LB@@LB@Position - mRNA 35 -- 66@LB@Position - sRNA 67 -- 98@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 87 -- 93@LB@
80	0.008443	0.3551	b3791	wecE	-14.19	0.039608	22 -- 66	14 -- 64	TDP-4-oxo-6-deoxy-D-glucose transaminase	_____________21______________67\n_____________\|_______________\|\n5'-GAC...ACCGC_______________GGUGA...CCC-3'\n______________GUACU_GGUUAUACA\n______________:\|\|\|\|_:\|\|:\|:\|\|\|\n______________UAUGA_UCAGUGUGU\n3'-UUU...GUGGU_____G_________ACUAC...UAG-5'\n_____________\|_______________\|\n_____________65______________13\n	185 -- 191	167 -- 173	-12.5686 kcal/mol	2.73267 kcal/mol	0.435744 kcal/mol	21 67@LB@ \| \|@LB@5'-GAC...ACCGC GGUGA...CCC-3'@LB@ GUACU GGUUAUACA@LB@ :\|\|\|\| :\|\|:\|:\|\|\|@LB@ UAUGA UCAGUGUGU@LB@3'-UUU...GUGGU G ACUAC...UAG-5'@LB@ \| \|@LB@ 65 13@LB@@LB@@LB@Energy -14.19 kcal/mol@LB@Hybridization Energy -12.5686 kcal/mol@LB@Unfolding Energy - mRNA 2.73267 kcal/mol@LB@Unfolding Energy - sRNA 0.435744 kcal/mol@LB@@LB@Position - mRNA 22 -- 66@LB@Position - sRNA 14 -- 64@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 167 -- 173@LB@
194	0.02283	0.3833	b3823	rhtC	-9.67	0.316154	216 -- 300	113 -- 178	threonine efflux pump	_____________215___________________301\n_____________\|_____________________\|\n5'-AGA...UAUUU____CC_______________CAUUG...GUU-3'\n______________CUCA__GUCGC_CAUGGUGCA\n______________\|\|\|\|__\|\|\|:\|_\|\|\|\|:\|\|\|\|\n______________GAGU__CAGUG_GUACUACGU\n3'-UUU...GUUAU___________U_________CCGUU...UAG-5'\n_____________\|_____________________\|\n_____________179___________________112\n	228 -- 234	161 -- 167	-23.3741 kcal/mol	7.13181 kcal/mol	4.79874 kcal/mol	215 301@LB@ \| \|@LB@5'-AGA...UAUUU CC CAUUG...GUU-3'@LB@ CUCA GUCGC CAUGGUGCA@LB@ \|\|\|\| \|\|\|:\| \|\|\|\|:\|\|\|\|@LB@ GAGU CAGUG GUACUACGU@LB@3'-UUU...GUUAU U CCGUU...UAG-5'@LB@ \| \|@LB@ 179 112@LB@@LB@@LB@Energy -9.67 kcal/mol@LB@Hybridization Energy -23.3741 kcal/mol@LB@Unfolding Energy - mRNA 7.13181 kcal/mol@LB@Unfolding Energy - sRNA 4.79874 kcal/mol@LB@@LB@Position - mRNA 216 -- 300@LB@Position - sRNA 113 -- 178@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 161 -- 167@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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