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
41	0.0008276	0.06626	b1218	chaC	-8.54	0.293650	119 -- 139	24 -- 45	cation transport regulator	_____________118____________________140\n_____________\|______________________\|\n5'-AUA...CGUUA________AAAAUG________AAAAU...CGC-3'\n______________GUGGUUUC______AGC_AGUA\n______________\|\|\|\|\|\|:\|______\|\|\|_\|\|:\|\n______________CACCAAGG______UCG_UCGU\n3'-UUU...UCCUC________ACCAUG___A____AAAAU...UCG-5'\n_____________\|______________________\|\n_____________46_____________________23\n	120 -- 126	38 -- 44	-17.6586 kcal/mol	4.55792 kcal/mol	4.55794 kcal/mol	118 140@LB@ \| \|@LB@5'-AUA...CGUUA AAAAUG AAAAU...CGC-3'@LB@ GUGGUUUC AGC AGUA@LB@ \|\|\|\|\|\|:\| \|\|\| \|\|:\|@LB@ CACCAAGG UCG UCGU@LB@3'-UUU...UCCUC ACCAUG A AAAAU...UCG-5'@LB@ \| \|@LB@ 46 23@LB@@LB@@LB@Energy -8.54 kcal/mol@LB@Hybridization Energy -17.6586 kcal/mol@LB@Unfolding Energy - mRNA 4.55792 kcal/mol@LB@Unfolding Energy - sRNA 4.55794 kcal/mol@LB@@LB@Position - mRNA 119 -- 139@LB@Position - sRNA 24 -- 45@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 38 -- 44@LB@
42	0.000828	0.06626	b2129	yehX	-13.83	0.023625	55 -- 85	15 -- 47	putative ABC transporter ATPase	_____________54________________________________86\n_____________\|_________________________________\|\n5'-GGU...GGCGC___C___________________UUUCCAG___CUGCU...UUG-3'\n______________AGG_GGUU_UUGGUGC_GCUGGU_______GGG\n______________\|\|\|_\|\|\|\|_:\|\|\|\|:\|_\|\|\|:\|:_______\|\|\|\n______________UCC_CCAA_GACCAUG_CGAUCG_______CCC\n3'-UUU...AUUCC___A____G_______U______UAAAAUA___AAUAC...UCG-5'\n_____________\|_________________________________\|\n_____________48________________________________14\n	63 -- 69	32 -- 38	-32.2293 kcal/mol	13.8239 kcal/mol	4.57348 kcal/mol	54 86@LB@ \| \|@LB@5'-GGU...GGCGC C UUUCCAG CUGCU...UUG-3'@LB@ AGG GGUU UUGGUGC GCUGGU GGG@LB@ \|\|\| \|\|\|\| :\|\|\|\|:\| \|\|\|:\|: \|\|\|@LB@ UCC CCAA GACCAUG CGAUCG CCC@LB@3'-UUU...AUUCC A G U UAAAAUA AAUAC...UCG-5'@LB@ \| \|@LB@ 48 14@LB@@LB@@LB@Energy -13.83 kcal/mol@LB@Hybridization Energy -32.2293 kcal/mol@LB@Unfolding Energy - mRNA 13.8239 kcal/mol@LB@Unfolding Energy - sRNA 4.57348 kcal/mol@LB@@LB@Position - mRNA 55 -- 85@LB@Position - sRNA 15 -- 47@LB@Position Seed - mRNA 63 -- 69@LB@Position Seed - sRNA 32 -- 38@LB@
43	0.0008959	0.07003	b3068	mug	-12.52	0.050096	232 -- 248	1 -- 17	G/U mismatch-specific DNA glycosylase; xanthine DNA glycosylase	_____________231_______________249\n_____________\|_________________\|\n5'-UGG...GUUAC____C_______G____AUCAA...CGG-3'\n______________GGGU_GUGUUUU_CGGU\n______________\|\|\|\|_:\|\|\|\|\|\|_\|:\|:\n______________CCCA_UACAAAA_GUCG\n3'-UUU...AAAUA____A_______A____-5'\n_____________\|________________\|\n_____________18_______________1\n	237 -- 243	6 -- 12	-17.5569 kcal/mol	4.10869 kcal/mol	0.931609 kcal/mol	231 249@LB@ \| \|@LB@5'-UGG...GUUAC C G AUCAA...CGG-3'@LB@ GGGU GUGUUUU CGGU@LB@ \|\|\|\| :\|\|\|\|\|\| \|:\|:@LB@ CCCA UACAAAA GUCG@LB@3'-UUU...AAAUA A A -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -12.52 kcal/mol@LB@Hybridization Energy -17.5569 kcal/mol@LB@Unfolding Energy - mRNA 4.10869 kcal/mol@LB@Unfolding Energy - sRNA 0.931609 kcal/mol@LB@@LB@Position - mRNA 232 -- 248@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 6 -- 12@LB@
44	0.0009392	0.07174	b3453	ugpB	-12.21	0.059079	239 -- 268	1 -- 32	sn-glycerol-3-phosphate ABC transporter periplasmic binding protein	_____________238_______________________________269\n_____________\|_________________________________\|\n5'-UUC...GCGCU___A________A______GA___CACA_____AGUGA...UGG-3'\n______________CGG_CUGGCGUU__AUGGG__AUG______GGC\n______________\|:\|_\|\|:\|\|:\|\|__\|\|\|\|\|__\|\|\|______:\|\|\n______________GUC_GAUCGUAA__UACCC__UAC______UCG\n3'-UUU...ACCAU____________AA_____AA___AAAAAG___-5'\n_____________\|________________________________\|\n_____________33_______________________________1\n	244 -- 250	22 -- 28	-24.6308 kcal/mol	10.9347 kcal/mol	1.49075 kcal/mol	238 269@LB@ \| \|@LB@5'-UUC...GCGCU A A GA CACA AGUGA...UGG-3'@LB@ CGG CUGGCGUU AUGGG AUG GGC@LB@ \|:\| \|\|:\|\|:\|\| \|\|\|\|\| \|\|\| :\|\|@LB@ GUC GAUCGUAA UACCC UAC UCG@LB@3'-UUU...ACCAU AA AA AAAAAG -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -12.21 kcal/mol@LB@Hybridization Energy -24.6308 kcal/mol@LB@Unfolding Energy - mRNA 10.9347 kcal/mol@LB@Unfolding Energy - sRNA 1.49075 kcal/mol@LB@@LB@Position - mRNA 239 -- 268@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 22 -- 28@LB@
45	0.001037	0.07744	b0857	potI	-11.49	0.084883	37 -- 88	3 -- 46	putrescine ABC transporter permease	_____________36______________________________________________________89\n_____________\|_______________________________________________________\|\n5'-CCG...UGCUC_________C________AUCAUGAUCGGGC____GC_____CAAGA________AUAAC...AUU-3'\n______________GGUGG__CC_GG_ACAGC_____________GCGU__UAUGG_____GUUUUUCA\n______________\|\|\|\|\|__\|\|_\|\|_\|\|\|\|\|_____________\|\|:\|__\|\|\|\|\|_____\|\|\|\|\|\|\|\|\n______________CCACC__GG_CC_UGUCG_____________CGUA__AUACC_____CAAAAAGU\n3'-UUU...UUCCU_____AA__A__A_____AU_______________AA_____CAAUA________CG-5'\n_____________\|_______________________________________________________\|\n_____________47______________________________________________________2\n	82 -- 88	3 -- 9	-33.7321 kcal/mol	17.6344 kcal/mol	4.60931 kcal/mol	36 89@LB@ \| \|@LB@5'-CCG...UGCUC C AUCAUGAUCGGGC GC CAAGA AUAAC...AUU-3'@LB@ GGUGG CC GG ACAGC GCGU UAUGG GUUUUUCA@LB@ \|\|\|\|\| \|\| \|\| \|\|\|\|\| \|\|:\| \|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ CCACC GG CC UGUCG CGUA AUACC CAAAAAGU@LB@3'-UUU...UUCCU AA A A AU AA CAAUA CG-5'@LB@ \| \|@LB@ 47 2@LB@@LB@@LB@Energy -11.49 kcal/mol@LB@Hybridization Energy -33.7321 kcal/mol@LB@Unfolding Energy - mRNA 17.6344 kcal/mol@LB@Unfolding Energy - sRNA 4.60931 kcal/mol@LB@@LB@Position - mRNA 37 -- 88@LB@Position - sRNA 3 -- 46@LB@Position Seed - mRNA 82 -- 88@LB@Position Seed - sRNA 3 -- 9@LB@
46	0.00106	0.07744	b3234	degQ	-13.26	0.033170	226 -- 262	1 -- 35	serine endoprotease periplasmic	_____________225____________________________________263\n_____________\|______________________________________\|\n5'-CUG...GUUGA______________AAG___C______ACUCUC_____GUCAU...UUG-3'\n______________GUGCA_UUAGCGUU___UGU_GGGUUA______UCGGC\n______________\|\|:\|\|_:\|\|\|\|:\|\|___\|:\|_\|\|\|\|\|\|______\|\|:\|\|\n______________CAUGU_GAUCGUAA___AUA_CCCAAU______AGUCG\n3'-UUU...AGGAC_____C________A____________ACAAAA_____-5'\n_____________\|_____________________________________\|\n_____________36____________________________________1\n	232 -- 238	22 -- 28	-28.0432 kcal/mol	13.2904 kcal/mol	1.49508 kcal/mol	225 263@LB@ \| \|@LB@5'-CUG...GUUGA AAG C ACUCUC GUCAU...UUG-3'@LB@ GUGCA UUAGCGUU UGU GGGUUA UCGGC@LB@ \|\|:\|\| :\|\|\|\|:\|\| \|:\| \|\|\|\|\|\| \|\|:\|\|@LB@ CAUGU GAUCGUAA AUA CCCAAU AGUCG@LB@3'-UUU...AGGAC C A ACAAAA -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -13.26 kcal/mol@LB@Hybridization Energy -28.0432 kcal/mol@LB@Unfolding Energy - mRNA 13.2904 kcal/mol@LB@Unfolding Energy - sRNA 1.49508 kcal/mol@LB@@LB@Position - mRNA 226 -- 262@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 22 -- 28@LB@
47	0.001093	0.07744	b0128	yadH	-6.67	0.521304	272 -- 286	25 -- 36	putative ABC transporter permease	_____________271_____________287\n_____________\|_______________\|\n5'-UUA...AUCUG_______ACG_____GCCGC...UCA-3'\n______________GGUGCAG___CUGGU\n______________\|\|\|:\|\|\|___\|\|:\|:\n______________CCAUGUC___GAUCG\n3'-UUU...AAGGA_______________UAAAA...UCG-5'\n_____________\|_______________\|\n_____________37______________24\n	272 -- 278	30 -- 36	-13.5693 kcal/mol	5.47586 kcal/mol	1.42738 kcal/mol	271 287@LB@ \| \|@LB@5'-UUA...AUCUG ACG GCCGC...UCA-3'@LB@ GGUGCAG CUGGU@LB@ \|\|\|:\|\|\| \|\|:\|:@LB@ CCAUGUC GAUCG@LB@3'-UUU...AAGGA UAAAA...UCG-5'@LB@ \| \|@LB@ 37 24@LB@@LB@@LB@Energy -6.67 kcal/mol@LB@Hybridization Energy -13.5693 kcal/mol@LB@Unfolding Energy - mRNA 5.47586 kcal/mol@LB@Unfolding Energy - sRNA 1.42738 kcal/mol@LB@@LB@Position - mRNA 272 -- 286@LB@Position - sRNA 25 -- 36@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 30 -- 36@LB@
48	0.001117	0.07744	b2829	ptsP	-13.12	0.035810	22 -- 37	14 -- 33	PEP-protein phosphotransferase enzyme I; GAF domain containing protein	_____________21___________________38\n_____________\|____________________\|\n5'-CCA...GUUUG____________________AAGUU...UGG-3'\n______________ACGGCUGGCG____AUGGGU\n______________\|\|:\|\|\|:\|\|:____\|\|\|\|\|\|\n______________UGUCGAUCGU____UACCCA\n3'-UUU...GACCA__________AAAA______AUACA...UCG-5'\n_____________\|____________________\|\n_____________34___________________13\n	25 -- 31	24 -- 30	-23.1334 kcal/mol	8.56068 kcal/mol	1.44884 kcal/mol	21 38@LB@ \| \|@LB@5'-CCA...GUUUG AAGUU...UGG-3'@LB@ ACGGCUGGCG AUGGGU@LB@ \|\|:\|\|\|:\|\|: \|\|\|\|\|\|@LB@ UGUCGAUCGU UACCCA@LB@3'-UUU...GACCA AAAA AUACA...UCG-5'@LB@ \| \|@LB@ 34 13@LB@@LB@@LB@Energy -13.12 kcal/mol@LB@Hybridization Energy -23.1334 kcal/mol@LB@Unfolding Energy - mRNA 8.56068 kcal/mol@LB@Unfolding Energy - sRNA 1.44884 kcal/mol@LB@@LB@Position - mRNA 22 -- 37@LB@Position - sRNA 14 -- 33@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 24 -- 30@LB@
49	0.001147	0.07744	b3039	ygiD	-13.27	0.032900	280 -- 298	15 -- 33	4 5- DOPA-extradiol-dioxygenase	_____________279_________________299\n_____________\|___________________\|\n5'-ACG...UACCC__________GAAGU____GA-3'\n______________GCAGCUGGCA_____UGGG\n______________:\|\|\|\|\|:\|\|\|_____\|\|\|\|\n______________UGUCGAUCGU_____ACCC\n3'-UUU...GACCA__________AAAAU____AAUAC...UCG-5'\n_____________\|___________________\|\n_____________34__________________14\n	283 -- 289	24 -- 30	-23.43 kcal/mol	8.71058 kcal/mol	1.44754 kcal/mol	279 299@LB@ \| \|@LB@5'-ACG...UACCC GAAGU GA-3'@LB@ GCAGCUGGCA UGGG@LB@ :\|\|\|\|\|:\|\|\| \|\|\|\|@LB@ UGUCGAUCGU ACCC@LB@3'-UUU...GACCA AAAAU AAUAC...UCG-5'@LB@ \| \|@LB@ 34 14@LB@@LB@@LB@Energy -13.27 kcal/mol@LB@Hybridization Energy -23.43 kcal/mol@LB@Unfolding Energy - mRNA 8.71058 kcal/mol@LB@Unfolding Energy - sRNA 1.44754 kcal/mol@LB@@LB@Position - mRNA 280 -- 298@LB@Position - sRNA 15 -- 33@LB@Position Seed - mRNA 283 -- 289@LB@Position Seed - sRNA 24 -- 30@LB@
50	0.001175	0.07744	b3543	dppB	-14.13	0.019609	196 -- 210	1 -- 17	dipeptide/heme ABC transporter permease	_____________195_______________211\n_____________\|_________________\|\n5'-CGG...AAUCC__________G______UUAUU...AUC-3'\n______________GGGUUAUGUU___CAGU\n______________\|\|\|\|\|\|\|\|\|\|___\|\|\|:\n______________CCCAAUACAA___GUCG\n3'-UUU...AAAUA__________AAA____-5'\n_____________\|________________\|\n_____________18_______________1\n	199 -- 205	8 -- 14	-17.9134 kcal/mol	2.84721 kcal/mol	0.931609 kcal/mol	195 211@LB@ \| \|@LB@5'-CGG...AAUCC G UUAUU...AUC-3'@LB@ GGGUUAUGUU CAGU@LB@ \|\|\|\|\|\|\|\|\|\| \|\|\|:@LB@ CCCAAUACAA GUCG@LB@3'-UUU...AAAUA AAA -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -14.13 kcal/mol@LB@Hybridization Energy -17.9134 kcal/mol@LB@Unfolding Energy - mRNA 2.84721 kcal/mol@LB@Unfolding Energy - sRNA 0.931609 kcal/mol@LB@@LB@Position - mRNA 196 -- 210@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 8 -- 14@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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