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
196	0.0235	0.3833	b3105	yhaJ	-11.17	0.163135	292 -- 299	86 -- 93	LysR family putative transcriptional regulator	_____________291______300\n_____________\|________\|\n5'-CGG...UGAGC________G-3'\n______________UGGGACGC\n______________\|\|\|\|\|\|\|\|\n______________ACCCUGCG\n3'-UUU...GCAAC________AAUUG...UAG-5'\n_____________\|________\|\n_____________94_______85\n	293 -- 299	86 -- 92	-14.7688 kcal/mol	2.10679 kcal/mol	4.21973 kcal/mol	291 300@LB@ \| \|@LB@5'-CGG...UGAGC G-3'@LB@ UGGGACGC@LB@ \|\|\|\|\|\|\|\|@LB@ ACCCUGCG@LB@3'-UUU...GCAAC AAUUG...UAG-5'@LB@ \| \|@LB@ 94 85@LB@@LB@@LB@Energy -11.17 kcal/mol@LB@Hybridization Energy -14.7688 kcal/mol@LB@Unfolding Energy - mRNA 2.10679 kcal/mol@LB@Unfolding Energy - sRNA 4.21973 kcal/mol@LB@@LB@Position - mRNA 292 -- 299@LB@Position - sRNA 86 -- 93@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 86 -- 92@LB@
165	0.01884	0.3812	b3291	mscL	-11.12	0.167422	252 -- 267	193 -- 208	mechanosensitive channel protein high conductance	_____________251_____268\n_____________\|_______\|\n5'-UGU...UGUCG_______AGGGA...UCU-3'\n______________GCUUCAU\n______________\|\|\|\|\|\|\|\n______________CGAAGUA\n3'-UUU...GGGAA_______G-5'\n_____________\|_______\|\n_____________209_____192\n	182 -- 188	2 -- 8	-9.41561 kcal/mol	2.23742 kcal/mol	0.70263 kcal/mol	251 268@LB@ \| \|@LB@5'-UGU...UGUCG AGGGA...UCU-3'@LB@ GCUUCAU@LB@ \|\|\|\|\|\|\|@LB@ CGAAGUA@LB@3'-UUU...GGGAA G-5'@LB@ \| \|@LB@ 209 192@LB@@LB@@LB@Energy -11.12 kcal/mol@LB@Hybridization Energy -9.41561 kcal/mol@LB@Unfolding Energy - mRNA 2.23742 kcal/mol@LB@Unfolding Energy - sRNA 0.70263 kcal/mol@LB@@LB@Position - mRNA 252 -- 267@LB@Position - sRNA 193 -- 208@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 2 -- 8@LB@
191	0.02237	0.3833	b1658	purR	-11.05	0.172432	254 -- 265	163 -- 174	transcriptional repressor hypoxanthine-binding	_____________253_______________266\n_____________\|_________________\|\n5'-UUU...CUACA___GU____________CAACA...GCA-3'\n______________ACU__GUCACACGUGAU\n______________\|\|\|__\|\|\|\|\|\|\|:\|\|\|\|\n______________UGA__CAGUGUGUACUA\n3'-UUU...GGUUA___GU____________CGUCC...UAG-5'\n_____________\|_________________\|\n_____________175_______________162\n	259 -- 265	163 -- 169	-20.3148 kcal/mol	3.57431 kcal/mol	4.30742 kcal/mol	253 266@LB@ \| \|@LB@5'-UUU...CUACA GU CAACA...GCA-3'@LB@ ACU GUCACACGUGAU@LB@ \|\|\| \|\|\|\|\|\|\|:\|\|\|\|@LB@ UGA CAGUGUGUACUA@LB@3'-UUU...GGUUA GU CGUCC...UAG-5'@LB@ \| \|@LB@ 175 162@LB@@LB@@LB@Energy -11.05 kcal/mol@LB@Hybridization Energy -20.3148 kcal/mol@LB@Unfolding Energy - mRNA 3.57431 kcal/mol@LB@Unfolding Energy - sRNA 4.30742 kcal/mol@LB@@LB@Position - mRNA 254 -- 265@LB@Position - sRNA 163 -- 174@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 163 -- 169@LB@
129	0.01414	0.3575	b3579	yiaO	-11.03	0.174508	249 -- 273	50 -- 76	2 3-diketo-L-gulonate-binding periplasmic protein	_____________248_________________________274\n_____________\|___________________________\|\n5'-ACU...CGUCC____________C__UA__________UUGUU...AAA-3'\n______________UGGUUUUAUAUU_AU__UUAGUCGUAU\n______________\|\|:\|\|\|\|\|:\|::_\|\|__\|:\|\|\|\|::\|:\n______________ACUAAAAUGUGG_UA__AGUCAGUGUG\n3'-UUU...CGCCC____________U__UG__________UACUA...UAG-5'\n_____________\|___________________________\|\n_____________77__________________________49\n	132 -- 138	168 -- 174	-19.0823 kcal/mol	5.4875 kcal/mol	5.03533 kcal/mol	248 274@LB@ \| \|@LB@5'-ACU...CGUCC C UA UUGUU...AAA-3'@LB@ UGGUUUUAUAUU AU UUAGUCGUAU@LB@ \|\|:\|\|\|\|\|:\|:: \|\| \|:\|\|\|\|::\|:@LB@ ACUAAAAUGUGG UA AGUCAGUGUG@LB@3'-UUU...CGCCC U UG UACUA...UAG-5'@LB@ \| \|@LB@ 77 49@LB@@LB@@LB@Energy -11.03 kcal/mol@LB@Hybridization Energy -19.0823 kcal/mol@LB@Unfolding Energy - mRNA 5.4875 kcal/mol@LB@Unfolding Energy - sRNA 5.03533 kcal/mol@LB@@LB@Position - mRNA 249 -- 273@LB@Position - sRNA 50 -- 76@LB@Position Seed - mRNA 132 -- 138@LB@Position Seed - sRNA 168 -- 174@LB@
133	0.01432	0.3575	b2342	fadI	-11.00	0.176527	78 -- 109	125 -- 153	beta-ketoacyl-CoA thiolase anaerobic subunit	_____________77________________________________110\n_____________\|_________________________________\|\n5'-UCC...UCUCU__UU_____CUCUC________UAGC_______UUCCC...AUG-3'\n______________UC__CUUUU_____UGU_GUCA____UCCCACU\n______________\|\|__\|\|\|\|:_____\|\|:_\|\|\|\|____\|\|\|\|\|\|\|\n______________AG__GAAAG_____ACG_CAGU____AGGGUGA\n3'-UUU...CGUUC__UU_____UCUUA___C_______________CGUAG...UAG-5'\n_____________\|_________________________________\|\n_____________154_______________________________124\n	103 -- 109	125 -- 131	-19.0317 kcal/mol	1.6674 kcal/mol	9.91012 kcal/mol	77 110@LB@ \| \|@LB@5'-UCC...UCUCU UU CUCUC UAGC UUCCC...AUG-3'@LB@ UC CUUUU UGU GUCA UCCCACU@LB@ \|\| \|\|\|\|: \|\|: \|\|\|\| \|\|\|\|\|\|\|@LB@ AG GAAAG ACG CAGU AGGGUGA@LB@3'-UUU...CGUUC UU UCUUA C CGUAG...UAG-5'@LB@ \| \|@LB@ 154 124@LB@@LB@@LB@Energy -11.00 kcal/mol@LB@Hybridization Energy -19.0317 kcal/mol@LB@Unfolding Energy - mRNA 1.6674 kcal/mol@LB@Unfolding Energy - sRNA 9.91012 kcal/mol@LB@@LB@Position - mRNA 78 -- 109@LB@Position - sRNA 125 -- 153@LB@Position Seed - mRNA 103 -- 109@LB@Position Seed - sRNA 125 -- 131@LB@
124	0.0136	0.3575	b4065	yjcE	-10.85	0.188871	258 -- 289	125 -- 174	putative cation/proton antiporter	_____________257___________290\n_____________\|_____________\|\n5'-UAU...UGGUC_____U_______CCUUU...UGC-3'\n______________ACUCG_GUCAUGC\n______________\|\|\|\|:_\|\|\|\|::\|\n______________UGAGU_CAGUGUG\n3'-UUU...GGUUA_____________UACUA...UAG-5'\n_____________\|_____________\|\n_____________175___________124\n	267 -- 273	168 -- 174	-13.2629 kcal/mol	3.88311 kcal/mol	0.283892 kcal/mol	257 290@LB@ \| \|@LB@5'-UAU...UGGUC U CCUUU...UGC-3'@LB@ ACUCG GUCAUGC@LB@ \|\|\|\|: \|\|\|\|::\|@LB@ UGAGU CAGUGUG@LB@3'-UUU...GGUUA UACUA...UAG-5'@LB@ \| \|@LB@ 175 124@LB@@LB@@LB@Energy -10.85 kcal/mol@LB@Hybridization Energy -13.2629 kcal/mol@LB@Unfolding Energy - mRNA 3.88311 kcal/mol@LB@Unfolding Energy - sRNA 0.283892 kcal/mol@LB@@LB@Position - mRNA 258 -- 289@LB@Position - sRNA 125 -- 174@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 168 -- 174@LB@
43	0.003721	0.2912	b3232	zapE	-10.85	0.189153	236 -- 256	70 -- 90	divisome ATPase	_____________235___________257\n_____________\|_____________\|\n5'-AGG...AACGG____UU_______AACCG...AAA-3'\n______________CCUU__UUUCGUC\n______________\|\|\|\|__:\|\|\|:\|\|\n______________GGAA__GAAGUAG\n3'-UUU...GUGGG____C________-5'\n_____________\|____________\|\n_____________91___________70\n	146 -- 152	1 -- 7	-9.27362 kcal/mol	0.691484 kcal/mol	1.04836 kcal/mol	235 257@LB@ \| \|@LB@5'-AGG...AACGG UU AACCG...AAA-3'@LB@ CCUU UUUCGUC@LB@ \|\|\|\| :\|\|\|:\|\|@LB@ GGAA GAAGUAG@LB@3'-UUU...GUGGG C -5'@LB@ \| \|@LB@ 91 70@LB@@LB@@LB@Energy -10.85 kcal/mol@LB@Hybridization Energy -9.27362 kcal/mol@LB@Unfolding Energy - mRNA 0.691484 kcal/mol@LB@Unfolding Energy - sRNA 1.04836 kcal/mol@LB@@LB@Position - mRNA 236 -- 256@LB@Position - sRNA 70 -- 90@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 1 -- 7@LB@
143	0.01531	0.3575	b1641	slyB	-10.83	0.190300	158 -- 167	83 -- 92	outer membrane lipoprotein	_____________157____________________________168\n_____________\|______________________________\|\n5'-CCG...UCACA_______U______UGAC____AGG_____UUGCG...AAG-3'\n______________UAUGCCA_AUACUU____CAUG___GAUGC\n______________\|\|::\|\|\|_\|\|\|\|\|:____\|\|::___\|\|\|\|\|\n______________AUGUGGU_UAUGAG____GUGU___CUACG\n3'-UUU...CUAAA______________UCA_____GUA_____UCCGU...UAG-5'\n_____________\|______________________________\|\n_____________93_____________________________82\n	135 -- 141	182 -- 188	-20.8318 kcal/mol	7.22081 kcal/mol	7.72227 kcal/mol	157 168@LB@ \| \|@LB@5'-CCG...UCACA U UGAC AGG UUGCG...AAG-3'@LB@ UAUGCCA AUACUU CAUG GAUGC@LB@ \|\|::\|\|\| \|\|\|\|\|: \|\|:: \|\|\|\|\|@LB@ AUGUGGU UAUGAG GUGU CUACG@LB@3'-UUU...CUAAA UCA GUA UCCGU...UAG-5'@LB@ \| \|@LB@ 93 82@LB@@LB@@LB@Energy -10.83 kcal/mol@LB@Hybridization Energy -20.8318 kcal/mol@LB@Unfolding Energy - mRNA 7.22081 kcal/mol@LB@Unfolding Energy - sRNA 7.72227 kcal/mol@LB@@LB@Position - mRNA 158 -- 167@LB@Position - sRNA 83 -- 92@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 182 -- 188@LB@
149	0.01599	0.3612	b3236	mdh	-10.77	0.195799	223 -- 232	196 -- 205	malate dehydrogenase NAD(P)-binding	_____________222_____233\n_____________\|_______\|\n5'-GUU...AUGAA_______GUCCU...AUG-3'\n______________AGUCGCA\n______________\|\|\|\|:\|\|\n______________UCAGUGU\n3'-UUU...AUGAG_______GUACU...UAG-5'\n_____________\|_______\|\n_____________206_____195\n	206 -- 212	169 -- 175	-8.87418 kcal/mol	1.40028 kcal/mol	0.26566 kcal/mol	222 233@LB@ \| \|@LB@5'-GUU...AUGAA GUCCU...AUG-3'@LB@ AGUCGCA@LB@ \|\|\|\|:\|\|@LB@ UCAGUGU@LB@3'-UUU...AUGAG GUACU...UAG-5'@LB@ \| \|@LB@ 206 195@LB@@LB@@LB@Energy -10.77 kcal/mol@LB@Hybridization Energy -8.87418 kcal/mol@LB@Unfolding Energy - mRNA 1.40028 kcal/mol@LB@Unfolding Energy - sRNA 0.26566 kcal/mol@LB@@LB@Position - mRNA 223 -- 232@LB@Position - sRNA 196 -- 205@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 169 -- 175@LB@
39	0.003509	0.2912	b1293	sapB	-10.75	0.197427	9 -- 16	196 -- 203	antimicrobial peptide transport ABC transporter permease	_____________8____________17\n_____________\|____________\|\n5'-UCG...UAUUU_______CA___GC-3'\n______________CACCCCU__UGC\n______________\|\|\|\|\|\|:__\|\|\|\n______________GUGGGGG__ACG\n3'-UUU...ACCCC_______A____AAGUAG-5'\n_____________\|____________\|\n_____________204__________195\n	287 -- 293	11 -- 17	-15.5024 kcal/mol	0.267702 kcal/mol	6.55606 kcal/mol	8 17@LB@ \| \|@LB@5'-UCG...UAUUU CA GC-3'@LB@ CACCCCU UGC@LB@ \|\|\|\|\|\|: \|\|\|@LB@ GUGGGGG ACG@LB@3'-UUU...ACCCC A AAGUAG-5'@LB@ \| \|@LB@ 204 195@LB@@LB@@LB@Energy -10.75 kcal/mol@LB@Hybridization Energy -15.5024 kcal/mol@LB@Unfolding Energy - mRNA 0.267702 kcal/mol@LB@Unfolding Energy - sRNA 6.55606 kcal/mol@LB@@LB@Position - mRNA 9 -- 16@LB@Position - sRNA 196 -- 203@LB@Position Seed - mRNA 287 -- 293@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)

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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