Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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
71	0.001416	0.07026	b0880	cspD	-7.58	0.355655	51 -- 57	1 -- 7	inhibitor of DNA replication cold shock protein homolog	_____________50______58\n_____________\|_______\|\n5'-AUC...AUUCA_______CCCUU...CCA-3'\n______________UACCUGC\n______________:\|\|\|\|\|\|\n______________GUGGACG\n3'-UUU...CGUAA_______-5'\n_____________\|______\|\n_____________8______1\n	51 -- 57	1 -- 7	-10.3464 kcal/mol	0.429757 kcal/mol	2.34039 kcal/mol	50 58@LB@ \| \|@LB@5'-AUC...AUUCA CCCUU...CCA-3'@LB@ UACCUGC@LB@ :\|\|\|\|\|\|@LB@ GUGGACG@LB@3'-UUU...CGUAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -7.58 kcal/mol@LB@Hybridization Energy -10.3464 kcal/mol@LB@Unfolding Energy - mRNA 0.429757 kcal/mol@LB@Unfolding Energy - sRNA 2.34039 kcal/mol@LB@@LB@Position - mRNA 51 -- 57@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 51 -- 57@LB@Position Seed - sRNA 1 -- 7@LB@
72	0.001523	0.07451	b2296	ackA	-11.55	0.045253	141 -- 168	13 -- 36	acetate kinase A and propionate kinase 2	_____________140__________________________169\n_____________\|____________________________\|\n5'-AUU...AUCAU____U____U____G___CCC_______UUUUU...UAG-3'\n______________GCGC_ACGC_CUAU_GCU___UGACGUU\n______________\|\|\|\|_\|\|\|\|_\|:\|\|_\|\|\|___\|\|\|\|\|\|\|\n______________CGCG_UGCG_GGUA_CGA___ACUGCAA\n3'-UUU...UACCU____U_________G_____________CGUAA...ACG-5'\n_____________\|____________________________\|\n_____________37___________________________12\n	162 -- 168	13 -- 19	-30.8127 kcal/mol	7.01729 kcal/mol	12.2493 kcal/mol	140 169@LB@ \| \|@LB@5'-AUU...AUCAU U U G CCC UUUUU...UAG-3'@LB@ GCGC ACGC CUAU GCU UGACGUU@LB@ \|\|\|\| \|\|\|\| \|:\|\| \|\|\| \|\|\|\|\|\|\|@LB@ CGCG UGCG GGUA CGA ACUGCAA@LB@3'-UUU...UACCU U G CGUAA...ACG-5'@LB@ \| \|@LB@ 37 12@LB@@LB@@LB@Energy -11.55 kcal/mol@LB@Hybridization Energy -30.8127 kcal/mol@LB@Unfolding Energy - mRNA 7.01729 kcal/mol@LB@Unfolding Energy - sRNA 12.2493 kcal/mol@LB@@LB@Position - mRNA 141 -- 168@LB@Position - sRNA 13 -- 36@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 13 -- 19@LB@
73	0.001571	0.0758	b3746	ravA	-8.41	0.246327	240 -- 262	54 -- 75	hexameric AAA+ MoxR family ATPase putative molecular chaperone	_____________239_____________________263\n_____________\|_______________________\|\n5'-UGA...CCCGC___A_____UC___G________GCUUU...UAU-3'\n______________CUG_GCAGU__GUU_GAAAAGGG\n______________\|\|:_\|\|\|\|\|__:\|\|_:\|\|\|\|:\|\|\n______________GAU_CGUCA__UAA_UUUUUUCC\n3'-UUU...AACAC___A_____U____G________UUCAU...ACG-5'\n_____________\|_______________________\|\n_____________76______________________53\n	256 -- 262	54 -- 60	-19.2007 kcal/mol	7.09588 kcal/mol	3.69534 kcal/mol	239 263@LB@ \| \|@LB@5'-UGA...CCCGC A UC G GCUUU...UAU-3'@LB@ CUG GCAGU GUU GAAAAGGG@LB@ \|\|: \|\|\|\|\| :\|\| :\|\|\|\|:\|\|@LB@ GAU CGUCA UAA UUUUUUCC@LB@3'-UUU...AACAC A U G UUCAU...ACG-5'@LB@ \| \|@LB@ 76 53@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -19.2007 kcal/mol@LB@Unfolding Energy - mRNA 7.09588 kcal/mol@LB@Unfolding Energy - sRNA 3.69534 kcal/mol@LB@@LB@Position - mRNA 240 -- 262@LB@Position - sRNA 54 -- 75@LB@Position Seed - mRNA 256 -- 262@LB@Position Seed - sRNA 54 -- 60@LB@
74	0.001758	0.08273	b4012	yjaB	-8.69	0.215298	234 -- 243	51 -- 60	GNAT-family putative N-acetyltransferase; acetyl coenzyme A-binding protein	_____________233________244\n_____________\|__________\|\n5'-AAG...AUGAG__________AACUC...CAG-3'\n______________GAAGGGGAGG\n______________:\|\|::\|\|\|:\|\n______________UUUUUCCUUC\n3'-UUU...UAAGU__________AUUCU...ACG-5'\n_____________\|__________\|\n_____________61_________50\n	237 -- 243	51 -- 57	-10.2171 kcal/mol	0.810771 kcal/mol	0.715621 kcal/mol	233 244@LB@ \| \|@LB@5'-AAG...AUGAG AACUC...CAG-3'@LB@ GAAGGGGAGG@LB@ :\|\|::\|\|\|:\|@LB@ UUUUUCCUUC@LB@3'-UUU...UAAGU AUUCU...ACG-5'@LB@ \| \|@LB@ 61 50@LB@@LB@@LB@Energy -8.69 kcal/mol@LB@Hybridization Energy -10.2171 kcal/mol@LB@Unfolding Energy - mRNA 0.810771 kcal/mol@LB@Unfolding Energy - sRNA 0.715621 kcal/mol@LB@@LB@Position - mRNA 234 -- 243@LB@Position - sRNA 51 -- 60@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 51 -- 57@LB@
75	0.001837	0.08273	b1816	yoaE	-14.98	0.004573	118 -- 155	1 -- 35	putative membrane protein/conserved protein	_____________117____________________________________156\n_____________\|______________________________________\|\n5'-GAU...CUCUA___C__A___U_______C__U___U____A_______AUUAU...UUC-3'\n______________UGC_GC_CCU_UCGUUUG_AU_UUG_CGUU_CGCCUGC\n______________:\|\|_:\|_\|\|:_\|\|\|:\|\|\|_\|:_\|\|\|_\|:\|\|_\|:\|\|\|\|\|\n______________GCG_UG_GGG_AGCGAAC_UG_AAC_GUAA_GUGGACG\n3'-UUU...ACCUC___U__C___U__________C________________-5'\n_____________\|_____________________________________\|\n_____________36____________________________________1\n	149 -- 155	1 -- 7	-36.6264 kcal/mol	6.36146 kcal/mol	15.286 kcal/mol	117 156@LB@ \| \|@LB@5'-GAU...CUCUA C A U C U U A AUUAU...UUC-3'@LB@ UGC GC CCU UCGUUUG AU UUG CGUU CGCCUGC@LB@ :\|\| :\| \|\|: \|\|\|:\|\|\| \|: \|\|\| \|:\|\| \|:\|\|\|\|\|@LB@ GCG UG GGG AGCGAAC UG AAC GUAA GUGGACG@LB@3'-UUU...ACCUC U C U C -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -14.98 kcal/mol@LB@Hybridization Energy -36.6264 kcal/mol@LB@Unfolding Energy - mRNA 6.36146 kcal/mol@LB@Unfolding Energy - sRNA 15.286 kcal/mol@LB@@LB@Position - mRNA 118 -- 155@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 1 -- 7@LB@
76	0.001842	0.08273	b1717	rpmI	-9.61	0.135308	218 -- 256	48 -- 92	50S ribosomal subunit protein L35	_____________217___________________________________________257\n_____________\|_____________________________________________\|\n5'-GCG...AAGAC_____________GC_____A___C____________ACC_____AGGUG...UGA-3'\n______________CGUACG___CGGU__UGCUA_GCG____UUCAAAAAA___GGUAA\n______________\|\|\|\|\|\|___\|::\|__\|\|\|\|\|_\|\|:____\|\|\|\|\|\|\|\|\|___:\|\|\|\|\n______________GCAUGC___GUUA__ACGAU_CGU____AAGUUUUUU___UCAUU\n3'-UUU...CCGCA______UUA____AC_____A___CAUU_________CCU_____CUGUU...ACG-5'\n_____________\|_____________________________________________\|\n_____________93____________________________________________47\n	242 -- 248	56 -- 62	-26.2826 kcal/mol	11.8203 kcal/mol	4.85131 kcal/mol	217 257@LB@ \| \|@LB@5'-GCG...AAGAC GC A C ACC AGGUG...UGA-3'@LB@ CGUACG CGGU UGCUA GCG UUCAAAAAA GGUAA@LB@ \|\|\|\|\|\| \|::\| \|\|\|\|\| \|\|: \|\|\|\|\|\|\|\|\| :\|\|\|\|@LB@ GCAUGC GUUA ACGAU CGU AAGUUUUUU UCAUU@LB@3'-UUU...CCGCA UUA AC A CAUU CCU CUGUU...ACG-5'@LB@ \| \|@LB@ 93 47@LB@@LB@@LB@Energy -9.61 kcal/mol@LB@Hybridization Energy -26.2826 kcal/mol@LB@Unfolding Energy - mRNA 11.8203 kcal/mol@LB@Unfolding Energy - sRNA 4.85131 kcal/mol@LB@@LB@Position - mRNA 218 -- 256@LB@Position - sRNA 48 -- 92@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 56 -- 62@LB@
77	0.00185	0.08273	b2325	yfcL	-11.04	0.061434	190 -- 213	35 -- 57	uncharacterized protein	_____________189______________________214\n_____________\|________________________\|\n5'-AAC...ACAAU______AG________CGC_____UUGAA...GCC-3'\n______________GAGGAA__AAGAUGAU___GGAGU\n______________:\|\|\|\|\|__\|\|\|\|::\|\|___\|\|\|\|:\n______________UUCCUU__UUCUGUUA___CCUCG\n3'-UUU...GUUUU______CA________UA______CGUUG...ACG-5'\n_____________\|________________________\|\n_____________58_______________________34\n	199 -- 205	42 -- 48	-19.5886 kcal/mol	4.3321 kcal/mol	4.1846 kcal/mol	189 214@LB@ \| \|@LB@5'-AAC...ACAAU AG CGC UUGAA...GCC-3'@LB@ GAGGAA AAGAUGAU GGAGU@LB@ :\|\|\|\|\| \|\|\|\|::\|\| \|\|\|\|:@LB@ UUCCUU UUCUGUUA CCUCG@LB@3'-UUU...GUUUU CA UA CGUUG...ACG-5'@LB@ \| \|@LB@ 58 34@LB@@LB@@LB@Energy -11.04 kcal/mol@LB@Hybridization Energy -19.5886 kcal/mol@LB@Unfolding Energy - mRNA 4.3321 kcal/mol@LB@Unfolding Energy - sRNA 4.1846 kcal/mol@LB@@LB@Position - mRNA 190 -- 213@LB@Position - sRNA 35 -- 57@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 42 -- 48@LB@
78	0.001866	0.08273	b2952	yggT	-14.70	0.005634	84 -- 104	37 -- 56	putative inner membrane protein; compensates for loss in K+ uptake	_____________83____________________105\n_____________\|_____________________\|\n5'-AGG...UCUCU_____U__C____________AGCCG...ACA-3'\n______________GGGAA_GU_GGACGAUAUGGA\n______________:\|\|\|\|_\|\|_:\|\|\|:\|\|\|\|\|\|\|\n______________UCCUU_CA_UCUGUUAUACCU\n3'-UUU...UUUUU________U____________CGCGU...ACG-5'\n_____________\|_____________________\|\n_____________57____________________36\n	98 -- 104	37 -- 43	-24.1681 kcal/mol	5.76987 kcal/mol	3.6645 kcal/mol	83 105@LB@ \| \|@LB@5'-AGG...UCUCU U C AGCCG...ACA-3'@LB@ GGGAA GU GGACGAUAUGGA@LB@ :\|\|\|\| \|\| :\|\|\|:\|\|\|\|\|\|\|@LB@ UCCUU CA UCUGUUAUACCU@LB@3'-UUU...UUUUU U CGCGU...ACG-5'@LB@ \| \|@LB@ 57 36@LB@@LB@@LB@Energy -14.70 kcal/mol@LB@Hybridization Energy -24.1681 kcal/mol@LB@Unfolding Energy - mRNA 5.76987 kcal/mol@LB@Unfolding Energy - sRNA 3.6645 kcal/mol@LB@@LB@Position - mRNA 84 -- 104@LB@Position - sRNA 37 -- 56@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 37 -- 43@LB@
79	0.001882	0.08273	b2219	atoS	-12.26	0.029240	6 -- 44	51 -- 94	sensory histidine kinase in two-component regulatory system with AtoC	_____________5_____________________________________________45\n_____________\|_____________________________________________\|\n______5'-UCAGG__________AA__A_____AA_______U__________C____CUCCG...AUA-3'\n______________GUUGUACGAA__GA____GC_____GGUA_UUCAAAGGGG_GAAG\n______________\|\|:\|\|\|\|\|\|\|__:\|____\|\|_____:\|\|\|_\|\|\|\|\|\|:::\|_\|\|\|\|\n______________CAGCAUGCUU__UU____CG_____UCAU_AAGUUUUUUC_CUUC\n3'-UUU...AGCCG__________AG__AACA__AUACG____U_______________AUUCU...ACG-5'\n_____________\|_____________________________________________\|\n_____________95____________________________________________50\n	9 -- 15	85 -- 91	-28.4119 kcal/mol	11.2894 kcal/mol	4.86774 kcal/mol	5 45@LB@ \| \|@LB@ 5'-UCAGG AA A AA U C CUCCG...AUA-3'@LB@ GUUGUACGAA GA GC GGUA UUCAAAGGGG GAAG@LB@ \|\|:\|\|\|\|\|\|\| :\| \|\| :\|\|\| \|\|\|\|\|\|:::\| \|\|\|\|@LB@ CAGCAUGCUU UU CG UCAU AAGUUUUUUC CUUC@LB@3'-UUU...AGCCG AG AACA AUACG U AUUCU...ACG-5'@LB@ \| \|@LB@ 95 50@LB@@LB@@LB@Energy -12.26 kcal/mol@LB@Hybridization Energy -28.4119 kcal/mol@LB@Unfolding Energy - mRNA 11.2894 kcal/mol@LB@Unfolding Energy - sRNA 4.86774 kcal/mol@LB@@LB@Position - mRNA 6 -- 44@LB@Position - sRNA 51 -- 94@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 85 -- 91@LB@
80	0.001886	0.08273	b3205	yhbJ	-9.88	0.117656	21 -- 27	1 -- 7	adaptor protein for GlmZ/GlmY sRNA decay glucosamine-6-phosphate-regulated; NTPase	_____________20______28\n_____________\|_______\|\n5'-CGG...AAACG_______AUACU...CCG-3'\n______________CACCUGC\n______________\|\|\|\|\|\|\|\n______________GUGGACG\n3'-UUU...CGUAA_______-5'\n_____________\|______\|\n_____________8______1\n	21 -- 27	1 -- 7	-13.6981 kcal/mol	1.48735 kcal/mol	2.34039 kcal/mol	20 28@LB@ \| \|@LB@5'-CGG...AAACG AUACU...CCG-3'@LB@ CACCUGC@LB@ \|\|\|\|\|\|\|@LB@ GUGGACG@LB@3'-UUU...CGUAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -13.6981 kcal/mol@LB@Unfolding Energy - mRNA 1.48735 kcal/mol@LB@Unfolding Energy - sRNA 2.34039 kcal/mol@LB@@LB@Position - mRNA 21 -- 27@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 21 -- 27@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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