Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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
182	0.01043	0.1919	b1235	rssB	-12.59	0.048266	47 -- 57	25 -- 36	PcnB-degradosome interaction factor; response regulator		_____________46___________58\n_____________\|____________\|\n5'-AAU...CGGCC____________AGUGG...CAA-3'\n______________GG_ACAGCUGGC\n______________\|\|_\|\|\|\|\|\|:\|\|\n______________CC_UGUCGAUCG\n3'-UUU...AAGGA__A_________UAAAA...UCG-5'\n_____________\|____________\|\n_____________37___________24\n	51 -- 57	25 -- 31	-17.7308 kcal/mol	3.71782 kcal/mol	1.42738 kcal/mol	46 58@LB@ \| \|@LB@5'-AAU...CGGCC AGUGG...CAA-3'@LB@ GG ACAGCUGGC@LB@ \|\| \|\|\|\|\|\|:\|\|@LB@ CC UGUCGAUCG@LB@3'-UUU...AAGGA A UAAAA...UCG-5'@LB@ \| \|@LB@ 37 24@LB@@LB@@LB@Energy -12.59 kcal/mol@LB@Hybridization Energy -17.7308 kcal/mol@LB@Unfolding Energy - mRNA 3.71782 kcal/mol@LB@Unfolding Energy - sRNA 1.42738 kcal/mol@LB@@LB@Position - mRNA 47 -- 57@LB@Position - sRNA 25 -- 36@LB@Position Seed - mRNA 51 -- 57@LB@Position Seed - sRNA 25 -- 31@LB@
183	0.01048	0.1919	b1250	kch	-17.60	0.001460	228 -- 258	1 -- 33	voltage-gated potassium channel		_____________227_______________________________259\n_____________\|_________________________________\|\n5'-AAC...AACAA_____AACAAA_________GACCC________ACGAC...UUA-3'\n______________ACAGC______UUUAUGGGU_______UUCGGC\n______________\|\|\|\|\|______\|\|\|\|\|\|\|\|\|_______\|\|\|:\|\|\n______________UGUCG______AAAUACCCA_______AAGUCG\n3'-UUU...GACCA_____AUCGUA_________AUACAAA______-5'\n_____________\|________________________________\|\n_____________34_______________________________1\n	241 -- 247	14 -- 20	-24.8286 kcal/mol	5.73827 kcal/mol	1.49313 kcal/mol	227 259@LB@ \| \|@LB@5'-AAC...AACAA AACAAA GACCC ACGAC...UUA-3'@LB@ ACAGC UUUAUGGGU UUCGGC@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\|\| \|\|\|:\|\|@LB@ UGUCG AAAUACCCA AAGUCG@LB@3'-UUU...GACCA AUCGUA AUACAAA -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -17.60 kcal/mol@LB@Hybridization Energy -24.8286 kcal/mol@LB@Unfolding Energy - mRNA 5.73827 kcal/mol@LB@Unfolding Energy - sRNA 1.49313 kcal/mol@LB@@LB@Position - mRNA 228 -- 258@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 14 -- 20@LB@
31	0.0004941	0.05357	b1272	sohB	-11.06	0.104388	188 -- 235	1 -- 51	inner membrane protein S49 peptidase family protein		_____________187__________________________________________________236\n_____________\|____________________________________________________\|\n5'-UGU...UAACC____U_____AC__G___A__U____U_UGAA_____UU_____________GAAAA...AAC-3'\n______________AAGG_GG_GG__UC_UGG_AU_GUUG_C____UAUGG____UGUUUUU_GGC\n______________\|\|\|\|_\|\|_\|\|__\|\|_\|\|\|_\|:_\|:\|:_\|____\|\|\|\|\|____\|\|\|\|\|\|\|_:\|\|\n______________UUCC_CC_CC__AG_ACC_UG_CGAU_G____AUACC____ACAAAAA_UCG\n3'-UUU...UCCGA____U__A__A___G___A__U____C_UAAA_____CAAU_______G___-5'\n_____________\|___________________________________________________\|\n_____________52__________________________________________________1\n	226 -- 232	5 -- 11	-30.2617 kcal/mol	14.5124 kcal/mol	4.69283 kcal/mol	187 236@LB@ \| \|@LB@5'-UGU...UAACC U AC G A U U UGAA UU GAAAA...AAC-3'@LB@ AAGG GG GG UC UGG AU GUUG C UAUGG UGUUUUU GGC@LB@ \|\|\|\| \|\| \|\| \|\| \|\|\| \|: \|:\|: \| \|\|\|\|\| \|\|\|\|\|\|\| :\|\|@LB@ UUCC CC CC AG ACC UG CGAU G AUACC ACAAAAA UCG@LB@3'-UUU...UCCGA U A A G A U C UAAA CAAU G -5'@LB@ \| \|@LB@ 52 1@LB@@LB@@LB@Energy -11.06 kcal/mol@LB@Hybridization Energy -30.2617 kcal/mol@LB@Unfolding Energy - mRNA 14.5124 kcal/mol@LB@Unfolding Energy - sRNA 4.69283 kcal/mol@LB@@LB@Position - mRNA 188 -- 235@LB@Position - sRNA 1 -- 51@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 5 -- 11@LB@
178	0.009929	0.1875	b1278	pgpB	-11.49	0.084643	145 -- 171	10 -- 41	phosphatidylglycerophosphatase B		_____________144______________________________172\n_____________\|________________________________\|\n5'-GUU...AAUUU_______AA_____________CA________AUUGU...AAC-3'\n______________UUCCUGG_____CUGGCGUUUU____GUUAUG\n______________\|\|\|\|\|\|\|_____\|\|:\|\|:\|\|\|\|____\|\|\|\|\|\|\n______________AAGGACC_____GAUCGUAAAA____CAAUAC\n3'-UUU...CCACC_______AUGUC__________UACC______AAAAA...UCG-5'\n_____________\|________________________________\|\n_____________42_______________________________9\n	157 -- 163	20 -- 26	-25.137 kcal/mol	9.03979 kcal/mol	4.60294 kcal/mol	144 172@LB@ \| \|@LB@5'-GUU...AAUUU AA CA AUUGU...AAC-3'@LB@ UUCCUGG CUGGCGUUUU GUUAUG@LB@ \|\|\|\|\|\|\| \|\|:\|\|:\|\|\|\| \|\|\|\|\|\|@LB@ AAGGACC GAUCGUAAAA CAAUAC@LB@3'-UUU...CCACC AUGUC UACC AAAAA...UCG-5'@LB@ \| \|@LB@ 42 9@LB@@LB@@LB@Energy -11.49 kcal/mol@LB@Hybridization Energy -25.137 kcal/mol@LB@Unfolding Energy - mRNA 9.03979 kcal/mol@LB@Unfolding Energy - sRNA 4.60294 kcal/mol@LB@@LB@Position - mRNA 145 -- 171@LB@Position - sRNA 10 -- 41@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 20 -- 26@LB@
136	0.005909	0.146	b1291	sapD	-11.34	0.091029	118 -- 151	12 -- 36	antimicrobial peptide ABC transporter ATPase		_____________117________________________________152\n_____________\|__________________________________\|\n5'-AUC...UGCCA________AAUUAUGAU______G____U_____ACCUC...GUG-3'\n______________GGUGCGGC_________UAGCGU_UUGU_GGUUA\n______________\|\|\|:\|:\|\|_________\|\|\|\|:\|_\|\|:\|_\|\|\|\|\|\n______________CCAUGUCG_________AUCGUA_AAUA_CCAAU\n3'-UUU...AAGGA_______________________A____C_____ACAAA...UCG-5'\n_____________\|__________________________________\|\n_____________37_________________________________11\n	119 -- 125	29 -- 35	-24.3443 kcal/mol	11.5428 kcal/mol	1.45699 kcal/mol	117 152@LB@ \| \|@LB@5'-AUC...UGCCA AAUUAUGAU G U ACCUC...GUG-3'@LB@ GGUGCGGC UAGCGU UUGU GGUUA@LB@ \|\|\|:\|:\|\| \|\|\|\|:\| \|\|:\| \|\|\|\|\|@LB@ CCAUGUCG AUCGUA AAUA CCAAU@LB@3'-UUU...AAGGA A C ACAAA...UCG-5'@LB@ \| \|@LB@ 37 11@LB@@LB@@LB@Energy -11.34 kcal/mol@LB@Hybridization Energy -24.3443 kcal/mol@LB@Unfolding Energy - mRNA 11.5428 kcal/mol@LB@Unfolding Energy - sRNA 1.45699 kcal/mol@LB@@LB@Position - mRNA 118 -- 151@LB@Position - sRNA 12 -- 36@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 29 -- 35@LB@
109	0.004204	0.1296	b1384	feaR	-11.47	0.085662	210 -- 231	1 -- 26	transcriptional activator for tynA and feaB		_____________209________________________232\n_____________\|__________________________\|\n5'-UGU...ACCCC___________AUA___AG_______AAUGG...CGG-3'\n______________GCA____GUGG___AUG__UUUCAGC\n______________\|\|\|____:\|\|\|___\|\|\|__\|\|\|\|\|\|\|\n______________CGU____UACC___UAC__AAAGUCG\n3'-UUU...UCGAU___AAAA____CAA___AA_______-5'\n_____________\|_________________________\|\n_____________27________________________1\n	225 -- 231	1 -- 7	-17.3605 kcal/mol	4.42522 kcal/mol	1.46544 kcal/mol	209 232@LB@ \| \|@LB@5'-UGU...ACCCC AUA AG AAUGG...CGG-3'@LB@ GCA GUGG AUG UUUCAGC@LB@ \|\|\| :\|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ CGU UACC UAC AAAGUCG@LB@3'-UUU...UCGAU AAAA CAA AA -5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -11.47 kcal/mol@LB@Hybridization Energy -17.3605 kcal/mol@LB@Unfolding Energy - mRNA 4.42522 kcal/mol@LB@Unfolding Energy - sRNA 1.46544 kcal/mol@LB@@LB@Position - mRNA 210 -- 231@LB@Position - sRNA 1 -- 26@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 1 -- 7@LB@
84	0.00278	0.1082	b1418	cybB	-11.15	0.099871	281 -- 297	37 -- 49	cytochrome b561		_____________280_______________298\n_____________\|_________________\|\n5'-AAC...GCAAU____UUUC_________UCC-3'\n______________GGAG____GUGGUUUCU\n______________\|\|\|\|____\|\|\|\|\|\|:\|\|\n______________CCUC____CACCAAGGA\n3'-UUU...CGAUU_________________CCAUG...UCG-5'\n_____________\|_________________\|\n_____________50________________36\n	291 -- 297	37 -- 43	-16.7846 kcal/mol	2.49998 kcal/mol	3.13428 kcal/mol	280 298@LB@ \| \|@LB@5'-AAC...GCAAU UUUC UCC-3'@LB@ GGAG GUGGUUUCU@LB@ \|\|\|\| \|\|\|\|\|\|:\|\|@LB@ CCUC CACCAAGGA@LB@3'-UUU...CGAUU CCAUG...UCG-5'@LB@ \| \|@LB@ 50 36@LB@@LB@@LB@Energy -11.15 kcal/mol@LB@Hybridization Energy -16.7846 kcal/mol@LB@Unfolding Energy - mRNA 2.49998 kcal/mol@LB@Unfolding Energy - sRNA 3.13428 kcal/mol@LB@@LB@Position - mRNA 281 -- 297@LB@Position - sRNA 37 -- 49@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 37 -- 43@LB@
169	0.009174	0.1803	b1467	narY	-12.55	0.049142	183 -- 194	25 -- 36	nitrate reductase 2 (NRZ) beta subunit		_____________182__________195\n_____________\|____________\|\n5'-CGC...GAUCA_______GA___GAAAA...GCG-3'\n______________GGUACAG__GGC\n______________\|\|\|\|\|\|\|__:\|\|\n______________CCAUGUC__UCG\n3'-UUU...AAGGA_______GA___UAAAA...UCG-5'\n_____________\|____________\|\n_____________37___________24\n	183 -- 189	30 -- 36	-16.0252 kcal/mol	2.04549 kcal/mol	1.42738 kcal/mol	182 195@LB@ \| \|@LB@5'-CGC...GAUCA GA GAAAA...GCG-3'@LB@ GGUACAG GGC@LB@ \|\|\|\|\|\|\| :\|\|@LB@ CCAUGUC UCG@LB@3'-UUU...AAGGA GA UAAAA...UCG-5'@LB@ \| \|@LB@ 37 24@LB@@LB@@LB@Energy -12.55 kcal/mol@LB@Hybridization Energy -16.0252 kcal/mol@LB@Unfolding Energy - mRNA 2.04549 kcal/mol@LB@Unfolding Energy - sRNA 1.42738 kcal/mol@LB@@LB@Position - mRNA 183 -- 194@LB@Position - sRNA 25 -- 36@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 30 -- 36@LB@
81	0.002689	0.1082	b1498	ydeN	-15.88	0.005981	253 -- 275	21 -- 44	putative Ser-type periplasmic non-aryl sulfatase	b3678 b3801	_____________252______________________276\n_____________\|________________________\|\n5'-AUU...GAUAC___CA___________________GCUGC...UAA-3'\n______________UGG__UCUGGUAUGGCU_GCAUUU\n______________\|\|\|__:\|\|\|\|\|\|::\|\|\|_\|\|\|\|\|\|\n______________ACC__GGACCAUGUCGA_CGUAAA\n3'-UUU...CCUCC___AA____________U______AUACC...UCG-5'\n_____________\|________________________\|\n_____________45_______________________20\n	263 -- 269	28 -- 34	-26.8614 kcal/mol	6.42389 kcal/mol	4.55918 kcal/mol	252 276@LB@ \| \|@LB@5'-AUU...GAUAC CA GCUGC...UAA-3'@LB@ UGG UCUGGUAUGGCU GCAUUU@LB@ \|\|\| :\|\|\|\|\|\|::\|\|\| \|\|\|\|\|\|@LB@ ACC GGACCAUGUCGA CGUAAA@LB@3'-UUU...CCUCC AA U AUACC...UCG-5'@LB@ \| \|@LB@ 45 20@LB@@LB@@LB@Energy -15.88 kcal/mol@LB@Hybridization Energy -26.8614 kcal/mol@LB@Unfolding Energy - mRNA 6.42389 kcal/mol@LB@Unfolding Energy - sRNA 4.55918 kcal/mol@LB@@LB@Position - mRNA 253 -- 275@LB@Position - sRNA 21 -- 44@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 28 -- 34@LB@
196	0.01135	0.1946	b1515	lsrD	-9.63	0.194390	56 -- 86	16 -- 44	autoinducer 2 import system permease protein		_____________55______________________________87\n_____________\|_______________________________\|\n5'-AGC...GGGUC_______GC___CGGU__________G____ACGCC...AUA-3'\n______________UGGUUCU__UGG____GCUGGUGUUU_AUGG\n______________\|\|\|\|\|\|:__\|\|\|____\|\|\|:\|::\|\|\|_\|\|\|\|\n______________ACCAAGG__ACC____CGAUCGUAAA_UACC\n3'-UUU...CCUCC____________AUGU__________A____CAAUA...UCG-5'\n_____________\|_______________________________\|\n_____________45______________________________15\n	56 -- 62	38 -- 44	-28.9595 kcal/mol	14.7558 kcal/mol	4.57147 kcal/mol	55 87@LB@ \| \|@LB@5'-AGC...GGGUC GC CGGU G ACGCC...AUA-3'@LB@ UGGUUCU UGG GCUGGUGUUU AUGG@LB@ \|\|\|\|\|\|: \|\|\| \|\|\|:\|::\|\|\| \|\|\|\|@LB@ ACCAAGG ACC CGAUCGUAAA UACC@LB@3'-UUU...CCUCC AUGU A CAAUA...UCG-5'@LB@ \| \|@LB@ 45 15@LB@@LB@@LB@Energy -9.63 kcal/mol@LB@Hybridization Energy -28.9595 kcal/mol@LB@Unfolding Energy - mRNA 14.7558 kcal/mol@LB@Unfolding Energy - sRNA 4.57147 kcal/mol@LB@@LB@Position - mRNA 56 -- 86@LB@Position - sRNA 16 -- 44@LB@Position Seed - mRNA 56 -- 62@LB@Position Seed - sRNA 38 -- 44@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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