Input and runtime details for job 7743500 (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 7743500 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:35:00 CET 2018
	CopraRNA Started		@ Fri Feb 16 21:27:12 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 06:56:30 CET 2018
	Post-Processing Finished		@ Sat Feb 17 06:56:38 CET 2018
	Job Completed		@ Sat Feb 17 06:57:11 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7743500&toolName=CopraRNA ( 30 days expiry )

Description of the job

PrrF1

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_002516 Pseudomonas aeruginosa PAO1

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
78	0.000864	0.05078	pa4263	rplC	-13.85	0.021626	50 -- 71	101 -- 122	50S ribosomal protein L3	_____________49_______________________72\n_____________\|________________________\|\n5'-CGA...CGGAU________C_______G_______AGCUC...AUC-3'\n______________AAAACCGU_GAU__GC_CUGAUGA\n______________\|\|\|\|\|\|\|\|_\|\|\|__\|\|_\|\|\|\|\|\|\|\n______________UUUUGGCA_CUA__CG_GACUACU\n3'-UUU...CCAGU____________AU__________CCUCU...GUU-5'\n_____________\|________________________\|\n_____________123______________________100\n	65 -- 71	101 -- 107	-22.5702 kcal/mol	6.47727 kcal/mol	2.24427 kcal/mol	49 72@LB@ \| \|@LB@5'-CGA...CGGAU C G AGCUC...AUC-3'@LB@ AAAACCGU GAU GC CUGAUGA@LB@ \|\|\|\|\|\|\|\| \|\|\| \|\| \|\|\|\|\|\|\|@LB@ UUUUGGCA CUA CG GACUACU@LB@3'-UUU...CCAGU AU CCUCU...GUU-5'@LB@ \| \|@LB@ 123 100@LB@@LB@@LB@Energy -13.85 kcal/mol@LB@Hybridization Energy -22.5702 kcal/mol@LB@Unfolding Energy - mRNA 6.47727 kcal/mol@LB@Unfolding Energy - sRNA 2.24427 kcal/mol@LB@@LB@Position - mRNA 50 -- 71@LB@Position - sRNA 101 -- 122@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 101 -- 107@LB@
85	0.001072	0.05733	pa4430	N/A	-13.41	0.028331	184 -- 204	101 -- 120	cytochrome b	_____________183___________________205\n_____________\|_____________________\|\n5'-ACC...GCGUG____AG__GAA__________ACAAG...UCU-3'\n______________GACC__GA___AGCCUGAUGA\n______________:\|\|\|__\|\|___\|\|\|\|\|\|\|\|\|\|\n______________UUGG__CU___UCGGACUACU\n3'-UUU...AGUUU____CA__AA___________CCUCU...GUU-5'\n_____________\|_____________________\|\n_____________121___________________100\n	198 -- 204	101 -- 107	-22.7142 kcal/mol	7.05943 kcal/mol	2.2437 kcal/mol	183 205@LB@ \| \|@LB@5'-ACC...GCGUG AG GAA ACAAG...UCU-3'@LB@ GACC GA AGCCUGAUGA@LB@ :\|\|\| \|\| \|\|\|\|\|\|\|\|\|\|@LB@ UUGG CU UCGGACUACU@LB@3'-UUU...AGUUU CA AA CCUCU...GUU-5'@LB@ \| \|@LB@ 121 100@LB@@LB@@LB@Energy -13.41 kcal/mol@LB@Hybridization Energy -22.7142 kcal/mol@LB@Unfolding Energy - mRNA 7.05943 kcal/mol@LB@Unfolding Energy - sRNA 2.2437 kcal/mol@LB@@LB@Position - mRNA 184 -- 204@LB@Position - sRNA 101 -- 120@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 101 -- 107@LB@
103	0.001681	0.07499	pa3587	metR	-12.26	0.055812	244 -- 261	101 -- 121	transcriptional regulator MetR	_____________243___________________262\n_____________\|_____________________\|\n5'-CAG...GCGCG______AC_____________AAGCC...UGU-3'\n______________AAGCCG_____AGCCUGGUGG\n______________\|\|:\|\|\|_____\|\|\|\|\|\|:\|\|:\n______________UUUGGC_____UCGGACUACU\n3'-UUU...CAGUU______ACUAA__________CCUCU...GUU-5'\n_____________\|_____________________\|\n_____________122___________________100\n	255 -- 261	101 -- 107	-20.5431 kcal/mol	6.04584 kcal/mol	2.24386 kcal/mol	243 262@LB@ \| \|@LB@5'-CAG...GCGCG AC AAGCC...UGU-3'@LB@ AAGCCG AGCCUGGUGG@LB@ \|\|:\|\|\| \|\|\|\|\|\|:\|\|:@LB@ UUUGGC UCGGACUACU@LB@3'-UUU...CAGUU ACUAA CCUCU...GUU-5'@LB@ \| \|@LB@ 122 100@LB@@LB@@LB@Energy -12.26 kcal/mol@LB@Hybridization Energy -20.5431 kcal/mol@LB@Unfolding Energy - mRNA 6.04584 kcal/mol@LB@Unfolding Energy - sRNA 2.24386 kcal/mol@LB@@LB@Position - mRNA 244 -- 261@LB@Position - sRNA 101 -- 121@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 101 -- 107@LB@
108	0.001802	0.07562	pa0365	N/A	-14.54	0.013920	243 -- 252	101 -- 110	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'	_____________242________253\n_____________\|__________\|\n5'-GCC...GACGC__________AAGUC...CCG-3'\n______________AGCCUGAUGA\n______________\|\|\|\|\|\|\|\|\|\|\n______________UCGGACUACU\n3'-UUU...ACUAA__________CCUCU...GUU-5'\n_____________\|__________\|\n_____________111________100\n	246 -- 252	101 -- 107	-17.5523 kcal/mol	0.900236 kcal/mol	2.11196 kcal/mol	242 253@LB@ \| \|@LB@5'-GCC...GACGC AAGUC...CCG-3'@LB@ AGCCUGAUGA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UCGGACUACU@LB@3'-UUU...ACUAA CCUCU...GUU-5'@LB@ \| \|@LB@ 111 100@LB@@LB@@LB@Energy -14.54 kcal/mol@LB@Hybridization Energy -17.5523 kcal/mol@LB@Unfolding Energy - mRNA 0.900236 kcal/mol@LB@Unfolding Energy - sRNA 2.11196 kcal/mol@LB@@LB@Position - mRNA 243 -- 252@LB@Position - sRNA 101 -- 110@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 101 -- 107@LB@
114	0.001956	0.07883	pa1616	N/A	-7.83	0.436748	16 -- 25	101 -- 110	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'	_____________15_________26\n_____________\|__________\|\n5'-GGC...ACGGC__________CUUUC...AGA-3'\n______________AGCCUGAUGG\n______________\|\|\|\|\|\|\|\|\|:\n______________UCGGACUACU\n3'-UUU...ACUAA__________CCUCU...GUU-5'\n_____________\|__________\|\n_____________111________100\n	19 -- 25	101 -- 107	-16.0192 kcal/mol	6.07491 kcal/mol	2.11196 kcal/mol	15 26@LB@ \| \|@LB@5'-GGC...ACGGC CUUUC...AGA-3'@LB@ AGCCUGAUGG@LB@ \|\|\|\|\|\|\|\|\|:@LB@ UCGGACUACU@LB@3'-UUU...ACUAA CCUCU...GUU-5'@LB@ \| \|@LB@ 111 100@LB@@LB@@LB@Energy -7.83 kcal/mol@LB@Hybridization Energy -16.0192 kcal/mol@LB@Unfolding Energy - mRNA 6.07491 kcal/mol@LB@Unfolding Energy - sRNA 2.11196 kcal/mol@LB@@LB@Position - mRNA 16 -- 25@LB@Position - sRNA 101 -- 110@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 101 -- 107@LB@
125	0.002365	0.08694	pa4303	tadZ	-11.60	0.080140	12 -- 30	101 -- 120	class 2: Function of highly similar gene experimentally demonstrated in another organism (and gene context consistent in terms of pathways its involved in (if known).	_____________11___________________31\n_____________\|____________________\|\n5'-UGG...AGGAC_____C__GCU_________UCGUC...GCG-3'\n______________GACCG_GA___G_CUGAUGA\n______________:\|\|\|\|_\|\|___\|_\|\|\|\|\|\|\|\n______________UUGGC_CU___C_GACUACU\n3'-UUU...AGUUU_____A__AAU_G_______CCUCU...GUU-5'\n_____________\|____________________\|\n_____________121__________________100\n	24 -- 30	101 -- 107	-18.3231 kcal/mol	4.48403 kcal/mol	2.2437 kcal/mol	11 31@LB@ \| \|@LB@5'-UGG...AGGAC C GCU UCGUC...GCG-3'@LB@ GACCG GA G CUGAUGA@LB@ :\|\|\|\| \|\| \| \|\|\|\|\|\|\|@LB@ UUGGC CU C GACUACU@LB@3'-UUU...AGUUU A AAU G CCUCU...GUU-5'@LB@ \| \|@LB@ 121 100@LB@@LB@@LB@Energy -11.60 kcal/mol@LB@Hybridization Energy -18.3231 kcal/mol@LB@Unfolding Energy - mRNA 4.48403 kcal/mol@LB@Unfolding Energy - sRNA 2.2437 kcal/mol@LB@@LB@Position - mRNA 12 -- 30@LB@Position - sRNA 101 -- 120@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 101 -- 107@LB@
127	0.002525	0.0912	pa3976	thiE	-9.31	0.244259	189 -- 204	101 -- 123	thiamine-phosphate pyrophosphorylase	_____________188_____________________205\n_____________\|_______________________\|\n5'-GCC...UCACU_______________________AACUG...GCC-3'\n______________GAGAGCC______AGCC_GAUGA\n______________:\|:\|:\|\|______\|\|\|\|_\|\|\|\|\|\n______________UUUUUGG______UCGG_CUACU\n3'-UUU...CCCAG_______CACUAA____A_____CCUCU...GUU-5'\n_____________\|_______________________\|\n_____________124_____________________100\n	189 -- 195	117 -- 123	-15.9836 kcal/mol	4.42969 kcal/mol	2.24445 kcal/mol	188 205@LB@ \| \|@LB@5'-GCC...UCACU AACUG...GCC-3'@LB@ GAGAGCC AGCC GAUGA@LB@ :\|:\|:\|\| \|\|\|\| \|\|\|\|\|@LB@ UUUUUGG UCGG CUACU@LB@3'-UUU...CCCAG CACUAA A CCUCU...GUU-5'@LB@ \| \|@LB@ 124 100@LB@@LB@@LB@Energy -9.31 kcal/mol@LB@Hybridization Energy -15.9836 kcal/mol@LB@Unfolding Energy - mRNA 4.42969 kcal/mol@LB@Unfolding Energy - sRNA 2.24445 kcal/mol@LB@@LB@Position - mRNA 189 -- 204@LB@Position - sRNA 101 -- 123@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 117 -- 123@LB@
135	0.002679	0.0912	pa0035	trpA	-9.18	0.258333	240 -- 261	101 -- 123	tryptophan synthase subunit alpha	_____________239_____________________262\n_____________\|_______________________\|\n5'-GAC...AGCAG________C_CCGC_________CCUUC...CCC-3'\n______________GAAAACCG_G_____CCUGGUGA\n______________:\|\|\|\|\|\|\|_\|_____\|\|\|\|:\|\|\|\n______________UUUUUGGC_C_____GGACUACU\n3'-UUU...CCCAG________A_UAAUC________CCUCU...GUU-5'\n_____________\|_______________________\|\n_____________124_____________________100\n	255 -- 261	101 -- 107	-19.6747 kcal/mol	8.2509 kcal/mol	2.24445 kcal/mol	239 262@LB@ \| \|@LB@5'-GAC...AGCAG C CCGC CCUUC...CCC-3'@LB@ GAAAACCG G CCUGGUGA@LB@ :\|\|\|\|\|\|\| \| \|\|\|\|:\|\|\|@LB@ UUUUUGGC C GGACUACU@LB@3'-UUU...CCCAG A UAAUC CCUCU...GUU-5'@LB@ \| \|@LB@ 124 100@LB@@LB@@LB@Energy -9.18 kcal/mol@LB@Hybridization Energy -19.6747 kcal/mol@LB@Unfolding Energy - mRNA 8.2509 kcal/mol@LB@Unfolding Energy - sRNA 2.24445 kcal/mol@LB@@LB@Position - mRNA 240 -- 261@LB@Position - sRNA 101 -- 123@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 101 -- 107@LB@
148	0.003408	0.1053	pa1533	N/A	-10.12	0.169364	218 -- 231	101 -- 120	nucleoid-associated protein	_____________217__________________232\n_____________\|____________________\|\n5'-AGA...GGCAU____________________AGCAG...CCG-3'\n______________GGCCG______GCCUGAUGA\n______________::\|\|\|______\|\|\|\|\|\|\|\|\|\n______________UUGGC______CGGACUACU\n3'-UUU...AGUUU_____ACUAAU_________CCUCU...GUU-5'\n_____________\|____________________\|\n_____________121__________________100\n	225 -- 231	101 -- 107	-19.3791 kcal/mol	7.01958 kcal/mol	2.2437 kcal/mol	217 232@LB@ \| \|@LB@5'-AGA...GGCAU AGCAG...CCG-3'@LB@ GGCCG GCCUGAUGA@LB@ ::\|\|\| \|\|\|\|\|\|\|\|\|@LB@ UUGGC CGGACUACU@LB@3'-UUU...AGUUU ACUAAU CCUCU...GUU-5'@LB@ \| \|@LB@ 121 100@LB@@LB@@LB@Energy -10.12 kcal/mol@LB@Hybridization Energy -19.3791 kcal/mol@LB@Unfolding Energy - mRNA 7.01958 kcal/mol@LB@Unfolding Energy - sRNA 2.2437 kcal/mol@LB@@LB@Position - mRNA 218 -- 231@LB@Position - sRNA 101 -- 120@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 101 -- 107@LB@
177	0.004514	0.1172	pa4639	N/A	-11.28	0.094804	222 -- 231	101 -- 110	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'	_____________221________232\n_____________\|__________\|\n5'-GUC...UGCUC__________CCGCA...UUA-3'\n______________AGCCUGAUGA\n______________\|\|\|\|\|\|\|\|\|\|\n______________UCGGACUACU\n3'-UUU...ACUAA__________CCUCU...GUU-5'\n_____________\|__________\|\n_____________111________100\n	225 -- 231	101 -- 107	-16.5496 kcal/mol	3.15503 kcal/mol	2.11196 kcal/mol	221 232@LB@ \| \|@LB@5'-GUC...UGCUC CCGCA...UUA-3'@LB@ AGCCUGAUGA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UCGGACUACU@LB@3'-UUU...ACUAA CCUCU...GUU-5'@LB@ \| \|@LB@ 111 100@LB@@LB@@LB@Energy -11.28 kcal/mol@LB@Hybridization Energy -16.5496 kcal/mol@LB@Unfolding Energy - mRNA 3.15503 kcal/mol@LB@Unfolding Energy - sRNA 2.11196 kcal/mol@LB@@LB@Position - mRNA 222 -- 231@LB@Position - sRNA 101 -- 110@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 101 -- 107@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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